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 and ...

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.

Homologs Homologous chromosomes or homologs are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during meiosis. Homologs have the same genes in the same loci, where they provide points along each chromosome th ...

of PtaRNA1 can be found in the bacterial families,

Betaproteobacteria ''Betaproteobacteria'' are a class of Gram-negative bacteria, and one of the six classes of the phylum '' Pseudomonadota'' (synonym Proteobacteria). Metabolism The ''Betaproteobacteria'' comprise over 75 genera and 400 species. Together, they ...

and

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

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

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

. In ''

Xanthomonas campestris ''Xanthomonas campestris'' is a gram-negative, obligate aerobic bacterium that is a member of the Xanthomonadaceae, a family of bacteria that are commonly known for their association with plant disease. This species includes ''Xanthomonas campe ...

'' 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 () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...

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 organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the e ...

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

toxin-antitoxin system A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed ...

s. In type I toxin-antitoxin systems, the

gene expression Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...

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 (; less commonly spelled procaryote) is a single-celled organism whose cell lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Ancient Greek (), meaning 'before', and (), meaning 'nut' ...

chromosomes and

s. The

secondary structure Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. 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 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 morpho ...

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 or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...

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