PtaRNA1 (

plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...

transferred

antisense RNA Antisense RNA (asRNA), also referred to as antisense transcript, natural antisense transcript (NAT) or antisense oligonucleotide, is a single stranded RNA that is complementary to a protein coding messenger RNA (mRNA) with which it hybridizes, and ...

) is a family of

non-coding RNAs 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 ...

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 locus (genetics), loci where they pr ...

of PtaRNA1 can be found in the bacterial families,

Betaproteobacteria Betaproteobacteria are a class of Gram-negative bacteria, and one of the eight classes of the phylum Pseudomonadota (synonym Proteobacteria). The ''Betaproteobacteria'' are a class comprising over 75 genera and 400 species of bacteria. Togeth ...

and

Gammaproteobacteria Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota (synonym Proteobacteria). It contains about 250 genera, which makes it the most genera-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically imp ...

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

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 ba ...

. In ''

Xanthomonas campestris ''Xanthomonas campestris'' is a bacterium that causes a variety of plant diseases, including "black rot" in cruciferous vegetables and bacterial wilt of turfgrass. It is also used in the commercial production of xanthan gum, a high-molecular-w ...

'' pv. ''vesicatoria'', this gene is annotated a
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 In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...

distribution. The distribution of ''ptaRNA1'' is not congruent with the phylogeny of the host species as it is with other sRNA families such as Yfr1 and Yfr2. This indicates that ptaRNA1 has undergone frequent

horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...

. These observations are in accordance with those made of Type I

toxin-antitoxin system A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a "toxin" protein and a corresponding "antitoxin". Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in mult ...

s. In type I toxin-antitoxin systems, the

gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. The ...

of a toxic protein is regulated by a small non-coding RNA. Type I toxin-antitoxin loci are frequently found in both

prokaryotic A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...

chromosomes and

s. The

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 ...

of ptaRNA1 is very similar to the ''E. coli''

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 Transcription refers to the ...

antisense RNA. FinP is an antisense regulator of the

cis-acting ''Cis''-regulatory elements (CREs) or ''Cis''-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morphoge ...

RNA element Traj, the structural similarities imply ptaRNA1 is likely to be part of a complex regulatory network. File:PtaRNA1 tree.jpg , A

phylogenetic tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

based on PtaRNA1 seed alignment. Class of the “host” species is shown by the symbols on the right hand side. Numbers indicate bootstrap values of the inner nodes.

References

External links

* {{Rfam, id=RF01811, name=PtaRNA1 Antisense RNA RNA antitoxins

Distribution and function

See also

References

External links