Yfr2 (cYanobacterial functional RNA-2
later published as Cyano-1 RNA motif)
is a family of
non-coding RNAs. 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
In genetics, a transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthe ...
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 ncRNAs in ''
Vibrio'' 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'' and ''
Synechococcus'' 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 (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
orthologs 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
rplLin 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
Yfr1 is a Cyanobacterial functional RNA that was identified by a comparative genome based screen for RNAs in cyanobacteria. Further analysis has shown that the RNA is well conserved and highly expressed in cyanobacteria. and is required for gr ...
, a
functional RNA which is
upregulated during
stress conditions.
Yfr families have now been identified up to yfr21.
See also
*
Non-coding RNA
*
Yfr1
Yfr1 is a Cyanobacterial functional RNA that was identified by a comparative genome based screen for RNAs in cyanobacteria. Further analysis has shown that the RNA is well conserved and highly expressed in cyanobacteria. and is required for gr ...
*
Cyano-2 RNA motif
The Cyano-2 RNA motif is a conserved RNA structure identified by bioinformatics. Cyano-2 RNAs are found in Cyanobacterial species classified within the genus ''Synechococcus''. Many terminal loops in the two conserved stem-loops contain the nuc ...
*
Cyano-S1 RNA motif
References
External links
*
Non-coding RNA
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