Yfr2 (cYanobacterial functional RNA-2 later published as Cyano-1 RNA motif) is a family of

non-coding RNA A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-c ...

s. Members of the Yrf2 family have been identified in almost all studied species of

cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blu ...

. The family was identified through a

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

screen of published cyanobacterial

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...

s, having previously been grouped in a family of Yfr2–5. The cyano-1 RNA motif family is essentially a synonym for Yfr2, although Cyano-1 does not include the terminator sequence and Yfr2 does. The function of this ncRNA is unknown, though it has been hypothesised that family members interact with

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

targets through kissing complexes using their highly conserved exposed central consensus element (CSE:

IUPAC The International Union of Pure and Applied Chemistry (IUPAC ) is an international federation of National Adhering Organizations working for the advancement of the chemical sciences, especially by developing nomenclature and terminology. It is ...

5′-RKT SGA AAC WHG GHM ASA M-3′). Earlier studies noted a similarity to

quorum sensing In biology, quorum sensing or quorum signalling (QS) is the ability to detect and respond to cell population density by gene regulation. As one example, QS enables bacteria to restrict the expression of specific genes to the high cell densities at ...

ncRNAs in ''

Vibrio ''Vibrio'' is a genus of Gram-negative bacteria, possessing a curved-rod (comma) shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Being highly salt tolerant and unable to survive ...

'' bacteria. The family can be divided into two subgroups, one found in

marine Marine is an adjective meaning of or pertaining to the sea or ocean. Marine or marines may refer to: Ocean * Maritime (disambiguation) * Marine art * Marine biology * Marine debris * Marine habitats * Marine life * Marine pollution Military * ...

cyanobacteria (e.g. the ''

Prochlorococcus ''Prochlorococcus'' is a genus of very small (0.6 μm) marine cyanobacteria with an unusual pigmentation ( chlorophyll ''a2'' and ''b2''). These bacteria belong to the photosynthetic picoplankton and are probably the most abundant photosynth ...

'' and ''

Synechococcus ''Synechococcus'' (from the Greek ''synechos'', in succession, and the Greek ''kokkos'', granule) is a unicellular cyanobacterium that is very widespread in the marine environment. Its size varies from 0.8 to 1.5 µm. The photosynthetic c ...

'' genera) and the other from

freshwater Fresh water or freshwater is any naturally occurring liquid or frozen water containing low concentrations of dissolved salts and other total dissolved solids. Although the term specifically excludes seawater and brackish water, it does include ...

cyanobacteria. Both subgroups have lengths of 63–100

nucleotides Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules w ...

(with the marine subgroup genes being on average 22nt longer), a conserved

5′ Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide pentose-sugar-ri ...

region and the characteristic Yfr2 CSE. Their

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

s differ, however, with Yfr2 from marine picocyanobacteria having an additional

stem loop Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when ...

. The position of Yfr2 genes is generally unconserved, but yfr2a

ortholog Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spec ...

s were identified as being located

3′ Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide pentose-sugar-ri ...

to the gene

50S ribosomal subunit 50 S is the larger subunit of the 70S ribosome of prokaryotes, i.e. bacteria and archaea. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins. It includes the 5S ribosomal RNA a ...

gen
rplL
in almost all marine cyanobacteria studied. In the genus ''Prochlorococcus'', Yfr2 genes are found adjacent to Yfr10 and a potential interaction between the two ncRNAs has been theorised. The initial bioinformatics scan which identified yfr2 also identified yfr1, a functional RNA which is

upregulated In the biological context of organisms' production of gene products, downregulation is the process by which a cell decreases the quantity of a cellular component, such as RNA or protein, in response to an external stimulus. The complementary proce ...

during stress conditions. Yfr families have now been identified up to yfr21.

References

External links

* Non-coding RNA {{molecular-biology-stub

See also

References

External links