The ''xerDC'' RNA motif is a conserved

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

structure that was discovered by bioinformatics. ''xerDC'' motif RNAs are found in

Clostridia The Clostridia are a highly polyphyletic class of Bacillota, including '' Clostridium'' and other similar genera. They are distinguished from the Bacilli by lacking aerobic respiration. They are obligate anaerobes and oxygen is toxic to them ...

. ''xerDC'' RNAs function as

cis-regulatory element ''Cis''-regulatory elements (CREs) or ''cis''-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morpho ...

s, in view of their positions upstream of protein-coding

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

s. ''xerDC'' RNAs are consistently located upstream of ''xerDC''

s. The precise functions of the

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

product of particular ''xerDC'' genes have not been established, but they are predicted to generally fit into a

recombinase Recombinases are genetic recombination enzymes. Site specific recombinases DNA recombinases are widely used in multicellular organisms to manipulate the structure of genomes, and to control gene expression. These enzymes, derived from bacteria ( ...

integrase Retroviral integrase (IN) is an enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme ...

role. Given this genetic arrangement, it is likely that ''xerDC'' RNAs function as

s. However, recombinases and integrases operate on

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

, which can sometimes be singled-stranded. Therefore, it is also possible that the ''xerDC'' motif actually operates at the level of single-stranded DNA. In terms of

secondary structure Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

, RNA and

are difficult to distinguish when only sequence information is available. ''xerDC'' RNAs sometimes partially overlap predicted genes. However, these genes are relatively small and their putative protein products are not similar to any known conserved

protein domain In molecular biology, a protein domain is a region of a protein's Peptide, polypeptide chain that is self-stabilizing and that Protein folding, folds independently from the rest. Each domain forms a compact folded Protein tertiary structure, thre ...

, suggesting that the genes might be

false positive A false positive is an error in binary classification in which a test result incorrectly indicates the presence of a condition (such as a disease when the disease is not present), while a false negative is the opposite error, where the test resu ...

predictions.

References

{{reflist Non-coding RNA