PtaRNA1 is a family of non-coding RNAs.
Homologs

Homology (biology)

Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...

 of PtaRNA1 can be found found in the proteobacteria

Proteobacteria

The Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera....

 families, Betaproteobacteria

Betaproteobacteria

Betaproteobacteria is a class of Proteobacteria. Betaproteobacteria are, like all Proteobacteria, gram-negative.The Betaproteobacteria consist of several groups of aerobic or facultative bacteria which are often highly versatile in their degradation capacities, but also contain chemolithotrophic...

 and Gammaproteobacteria

Gammaproteobacteria

Gammaproteobacteria is a class of several medically, ecologically and scientifically important groups of bacteria, such as the Enterobacteriaceae , Vibrionaceae and Pseudomonadaceae. An exceeding number of important pathogens belongs to this class, e.g...

. In all cases the PtaRNA1 is located anti-sense to a short protein-coding gene

Gene

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

. In Xanthomonas campestris

Xanthomonas campestris

Xanthomonas campestris is a bacterial species that causes a variety of plant diseases. Available from the NCPPB,and other international Culture collections such as ICMP, ATCC, and LMG in a purified form, it is used in the commercial production of a high-molecular-weight polysaccharide - xanthan...

pv. vesicatoria, this gene is annotated as XCV2162 and is included in the plasmid toxin family of proteins.

Distribution and function

Both PtaRNA1 and the adjacent coding gene, which only appear only in combination, have an erratic phylogenetic

Phylogenetics

In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...

 distribution.
The distribution of ptaRNA1 is not congruent with the phylogeny of the host species as it is with other sRNA

Srna

SRNA or Srna most commonly refers to:* Small RNA* Darijo Srna, a Croatian footballer who plays for Shakhtar Donetsk* Student Registered Nurse Anesthetist...

 families such as 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...

 and Yfr2

Yfr2

Yfr2 is a family of non-coding RNAs. Members of the Yrf2 family have been identified in almost all studied species of cyanobacteria...

.
This indicates that ptaRNA1 has undergone frequent horizontal gene transfer

Horizontal gene transfer

Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...

. These observations are in accordance with those made of Type I toxin-antitoxin system

Toxin-antitoxin system

A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a protein 'poison' and a corresponding 'antidote'. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid...

s.

In type I toxin-antitoxin systems, the gene expression

Gene expression

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...

 of a toxic protein is regulated by a small non-coding RNA

Srna

SRNA or Srna most commonly refers to:* Small RNA* Darijo Srna, a Croatian footballer who plays for Shakhtar Donetsk* Student Registered Nurse Anesthetist...

. Type I toxin-antitoxin loci

Locus (genetics)

In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...

 are frequently found in both prokaryotic

Prokaryote

The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

 chromosomes and plasmid

Plasmid

In microbiology and genetics, a plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA. They are double-stranded and, in many cases, circular...

s.
The 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...

 of ptaRNA1 is very similar to the E. coli

Escherichia coli

Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...

 FinP

FinP

FinP encodes an antisense non-coding RNA gene that is complementary to part of the TraJ 5' UTR. The FinOP system regulates the transfer of F-like plasmids. The traJ gene encodes a protein required for transcription from the major transfer promoter, pY. The FinO protein is essential for effective...

 antisense RNA. FinP is an antisense regulator of the cis-acting RNA element Traj

TraJ 5' UTR

The traJ 5' UTR is a cis acting RNA element which is involved in regulating plasmid transfer in bacteria.In conjugating bacteria the FinOP system regulates the transfer of F-like plasmids. The FinP gene encodes an antisense RNA product that is complementary to part of the 5' UTR of the traJ mRNA...

, the structural similarities imply ptaRNA1 is likely to be part of a complex regulatory network.