''malK'' RNA motifs are 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 ...

structures that were discovered by bioinformatics. They are defined by being consistently located upstream of ''malK''

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, which encode an

ATPase ATPases (, Adenosine 5'-TriPhosphatase, adenylpyrophosphatase, ATP monophosphatase, triphosphatase, ATP hydrolase, adenosine triphosphatase) are a class of enzymes that catalyze the decomposition of ATP into ADP and a free phosphate ion or ...

that is used by transporters whose

ligand In coordination chemistry, a ligand is an ion or molecule with a functional group that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's el ...

is likely a kind of

sugar Sugar is the generic name for sweet-tasting, soluble carbohydrates, many of which are used in food. Simple sugars, also called monosaccharides, include glucose Glucose is a sugar with the Chemical formula#Molecular formula, molecul ...

. Most of these genes are annotated either as transporting

maltose } Maltose ( or ), also known as maltobiose or malt sugar, is a disaccharide formed from two units of glucose joined with an α(1→4) bond. In the isomer isomaltose, the two glucose molecules are joined with an α(1→6) bond. Maltose is the tw ...

glycerol-3-phosphate ''sn''-Glycerol 3-phosphate is the organic ion with the formula HOCH2CH(OH)CH2OPO32-. It is one of two stereoisomers of the ester of dibasic phosphoric acid (HOPO32-) and glycerol. It is a component of bacterial and eukaryotic glycerophospholip ...

, however the substrate of the transporters associated with ''malK'' motif RNAs has not been experimentally determined. All known types of ''malK'' RNA motif are generally located nearby to the Shine-Dalgarno sequence of the downstream gene. Given their positions upstream of genes and proximal to Shine-Dalgarno sequences, ''malK'' RNA motifs likely 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, to regulate their associated ''malK'' genes. It is possible that they bind a sugar directly, and therefore function as

riboswitch In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in Translation (biology), production of the proteins encoded by the mRNA. Thus, an mRNA that contains a ribo ...

es, but it is equally possible that regulation is mediated via a

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 ...

factor, or some other mechanism. Three class of ''malK'' RNA motif have been found, and each class exhibits a completely unrelated structure, in terms of different conserved sequence features and a different conserved

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 ...

. ''malK''-I motifs 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 ...

, while ''malK''-II motifs are found in organisms within the

genus Genus (; : genera ) is a taxonomic rank above species and below family (taxonomy), family as used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In bino ...

Vibrio ''Vibrio'' is a genus of Gram-negative bacteria, which have a characteristic curved-rod (comma) shape, several species of which can cause foodborne infection or soft-tissue infection called Vibriosis. Infection is commonly associated with eati ...

''. ''malK''-III motifs have not yet (as of 2018) been identified in any classified organism but are known only from sequences isolated from

metagenomic Metagenomics is the study of all genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential. Metagenomics has allowed researchers to profile the microbial co ...

environmental samples.

References

{{Navbox , name = hide the gallery , title = Gallery of MalK RNA motifs , titlestyle = background:#e7dcc3 , state = autocollapse , list1 = {{Gallery , Image:RF03069.svg, malK-I Secondary structure taken from th
Rfam
database. Famil
RF03069
, Image:RF03008.svg, malK-II Secondary structure taken from th
Rfam
database. Famil
RF03008
, Image:RF03009.svg, malK-III Secondary structure taken from th
Rfam
database. Famil
RF03009
Non-coding RNA