The c4 antisense RNA is a

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- ...

used by certain

phage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek language, Greek φαγεῖν ('), meaning "to d ...

s that infect

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

. It was initially identified in the P1 and P7 phages of ''

E. coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...

''. The identification of c4 antisense RNAs solved the mystery of the mechanism for regulation of the ''ant''

gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

, which is an anti-repressor. The c4 antisense RNA has two regions, called a' and b' (see diagram), that are complementary to its targets. It has two targets, designated a1, b1 and a2, b2. The a1, b1 site is upstream of the c4 RNA, while the a2, b2 site is immediately downstream of it. The ''ant'' gene itself is immediately downstream of the a2, b2 target site. Binding of the a2, b2 site by the c4 antisense RNA represses the ''ant'' gene. The function of the a1, b1 site is unknown, but it was suggested that they might compete with the a2, b2 site for binding to c4 RNA.

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 combin ...

analysis uncovered many

homologs A couple of homologous chromosomes, or homologs, are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during fertilization. Homologs have the same genes in the same loci where they provide points alon ...

of the c4 antisense RNA that conserve the

secondary structure Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary struct ...

originally proposed for it. These homologs are present in purified phage particles of other phages, as well as bacterial

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 ...

s. The presence of c4 antisense RNAs in bacteria is to be expected, since the P1 and P7 phages are

temperate In geography, the temperate climates of Earth occur in the middle latitudes (23.5° to 66.5° N/S of Equator), which span between the tropics and the polar regions of Earth. These zones generally have wider temperature ranges throughout t ...

and can stably integrate into the host genome. The c4 antisense RNA consists of a three-stem junction. The terminus of the stem designated as "P2" very often conforms to highly stable

tetraloop Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. There are many variants of the tetraloop. The published ones include ANYA, CUYG, GNRA, UNAC and UNCG. Three types of tetraloops are ...

motifs that were previously elucidated, conforming to the consensus GNRA, UNCG or CUNG, where R represents either A or G nucleotides, and N can be any nucleotide. A rho-independent transcription terminator is often found that overlaps the c4 antisense RNA structure. Although RNAs often overlap transcription terminators to regulate transcription abundance, the information known about c4 antisense RNAs suggest that their terminator is more likely to be constitutive. Later bioinformatics work uncovered an additional set of RNAs called ("c4-2" RNAs) that appear to function as c4 antisense RNAs, but have a somewhat altered secondary structure. A conserved RNA structure adopted by the a1, b1 site was identified and called the "c4-a1b1" motif. This structure overlaps an earlier family of predicted RNAs called IsrK, which was identified among numerous RNA molecules that bind to the

Hfq protein The Hfq protein (also known as HF-I protein) encoded by the ''hfq'' gene was discovered in 1968 as an ''Escherichia coli'' host factor that was essential for replication of the bacteriophage Qβ. It is now clear that Hfq is an abundant bacterial R ...

, a protein that mediates many antisense RNA interactions. Later work on IsrK showed that its transcription was increased during late stationary phase of growth, or when cells are grown with low amounts of either

oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as we ...

magnesium Magnesium is a chemical element with the symbol Mg and atomic number 12. It is a shiny gray metal having a low density, low melting point and high chemical reactivity. Like the other alkaline earth metals (group 2 of the periodic ...

. It is unknown how this expression pattern might relate to the phage biology.

References

External links

* {{Rfam, id=RF01695, name=C4 antisense RNA Non-coding RNA