Non-coding RNA function and cations: studying the biological roles of the hammerhead ribozyme

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Aside from storing hereditary information, DNA and RNA are now known to have many more functions. Living organisms have a plethora of RNAs that control numerous processes in cells. A remarkable RNA, the hammerhead ribozyme, has a catalytic ability to self-cleave very efficiently. We recently discovered numerous hammerhead ribozymes in diverse types of organisms, including humans, archaea, bacteria and many DNA-viruses. In these species, the ribozyme's function is clearly different from the one known in plant RNA-viruses where it was discovered initially, but this function remains a mystery for now. However, we have indications that some of the novel hammerhead ribozymes are sensitive to specific types of metals, allowing bacteria or viruses to detect toxic metals in order to adapt to a hostile environment. In addition, the fact that this ribozyme is found in bacteria provides ideal model organisms to study its biological function. Through genetic, biochemical and bioinformatics studies of the hammerhead ribozyme, we will get a better understanding of the biology of metal resistance and phages (viruses of prokaryotes). Using targeted computational searches, we will uncover hammerhead ribozymes more likely to have regulatory roles. With biochemical tools, we will study some hammerhead ribozymes known to depend on metal ion concentration and others suspected to have regulatory roles related to metal ion sensing. In silico based investigation will be complemented with a novel screening technique to find other non-coding RNAs involved in metal sensing. Recent studies showing the possible use of non-coding RNAs as antibiotic targets exemplifies tangible applications for these discoveries. The high potential of non-coding RNAs is also applicable to their use in genetic engineering to improve regulation of gene expression in industrial use of bacteria.