Yfr2
Encyclopedia
Yfr2 is a family of non-coding RNA
s. Members of the Yrf2 family have been identified in almost all studied species of cyanobacteria. The family was identified through a bioinformatics
screen of published cyanobacterial genome
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
targets through kissing complexes using their highly conserved
exposed central consensus element
(CSE: IUPAC 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
cyanobacteria (e.g. the Prochlorococcus
and Synechococcus
genera) and the other from freshwater
cyanobacteria. Both subgroups have lengths of 63-100 nucleotides (with the marine subgroup genes being on average 22nt longer), a conserved 5' region and the characteristic Yfr2 CSE. Their secondary structure
s differ, however, with Yfr2 from marine picocyanobacteria having an additional stem loop. The position of Yfr2 genes is generally unconserved, but yfr2a orthologs were identified as being located 3' to the gene 50s ribosomal subunit
gene rplL in almost all marine cyanobacteria studied. In the Prochlorococcus genus, 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 during stress conditions
. Yfr families have now been identified up to yfr21.
Non-coding RNA
A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
s. Members of the Yrf2 family have been identified in almost all studied species of cyanobacteria. The family was identified through a bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
screen of published cyanobacterial genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
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
Terminator (genetics)
In genetics, a terminator, or transcription terminator is a section of genetic sequence that marks the end of gene or operon on genomic DNA for transcription.In prokaryotes, two classes of transcription terminators are known:...
and Yfr2 does.
The function of this ncRNA is unknown, though it has been hypothesised that family members interact with RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
targets through kissing complexes using their highly conserved
Conserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...
exposed central consensus element
Consensus sequence
In molecular biology and bioinformatics, consensus sequence refers to the most common nucleotide or amino acid at a particular position after multiple sequences are aligned. A consensus sequence is a way of representing the results of a multiple sequence alignment, where related sequences are...
(CSE: IUPAC 5'-RKT SGA
AAC WHG GHM ASA M-3'). Earlier studies noted a similarity to quorum sensing
Quorum sensing
Quorum sensing is a system of stimulus and response correlated to population density. Many species of bacteria use quorum sensing to coordinate gene expression according to the density of their local population. In similar fashion, some social insects use quorum sensing to determine where to nest...
ncRNAs in Vibrio
Vibrio
Vibrio is a genus of Gram-negative bacteria possessing a curved rod shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Typically found in saltwater, Vibrio are facultative anaerobes that test positive for oxidase and do not form...
bacteria.
The family can be divided into two subgroups, one found in marine
Marine (ocean)
Marine is an umbrella term. As an adjective it is usually applicable to things relating to the sea or ocean, such as marine biology, marine ecology and marine geology...
cyanobacteria (e.g. the Prochlorococcus
Prochlorococcus
Prochlorococcus is a genus of very small marine cyanobacteria with an unusual pigmentation . These bacteria belong to the photosynthetic picoplankton and are probably the most abundant photosynthetic organism on Earth....
and Synechococcus
Synechococcus
Synechococcus is a unicellular cyanobacterium that is very widespread in the marine environment. Its size varies from 0.8 µm to 1.5 µm...
genera) and the other from freshwater
Freshwater
Fresh water is naturally occurring water on the Earth's surface in ice sheets, ice caps, glaciers, bogs, ponds, lakes, rivers and streams, and underground as groundwater in aquifers and underground streams. Fresh water is generally characterized by having low concentrations of dissolved salts and...
cyanobacteria. Both subgroups have lengths of 63-100 nucleotides (with the marine subgroup genes being on average 22nt longer), a conserved 5' region and the characteristic Yfr2 CSE. Their secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
s differ, however, with Yfr2 from marine picocyanobacteria having an additional stem loop. The position of Yfr2 genes is generally unconserved, but yfr2a orthologs were identified as being located 3' to the gene 50s ribosomal subunit
50s
- Significant people :* Claudius, Roman Emperor * Nero, Roman Emperor * Kujula Kadphises, Kushan emperor* Paul of Tarsus, Christian evangelist* Emperor Ming of Han China...
gene rplL in almost all marine cyanobacteria studied. In the Prochlorococcus genus, 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
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...
, a functional RNA which is upregulated during stress conditions
Stress (biology)
Stress is a term in psychology and biology, borrowed from physics and engineering and first used in the biological context in the 1930s, which has in more recent decades become commonly used in popular parlance...
. Yfr families have now been identified up to yfr21.