RdlD RNA (regulator detected in LDR-D) is a family of small
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-c ...
s which repress the protein LdrD in a
type I toxin-antitoxin system. It was discovered in ''
Escherichia 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 ...
'' strain K-12 in a long direct
repeat (LDR) named LDR-D. This
locus
Locus (plural loci) is Latin for "place". It may refer to:
Entertainment
* Locus (comics), a Marvel Comics mutant villainess, a member of the Mutant Liberation Front
* ''Locus'' (magazine), science fiction and fantasy magazine
** ''Locus Award' ...
encodes two products: a 35
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
peptide toxin (ldrD) and a 60
nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...
RNA antitoxin.
The 374nt toxin
mRNA
In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein.
mRNA is ...
has a
half-life
Half-life (symbol ) is the time required for a quantity (of substance) to reduce to half of its initial value. The term is commonly used in nuclear physics to describe how quickly unstable atoms undergo radioactive decay or how long stable ato ...
of around 30 minutes while rdlD RNA has a half-life of only 2 minutes. This is in keeping with other type I toxin-antitoxin systems.
Northern blot
The northern blot, or RNA blot,Gilbert, S. F. (2000) Developmental Biology, 6th Ed. Sunderland MA, Sinauer Associates. is a technique used in molecular biology research to study gene expression by detection of RNA (or isolated mRNA) in a sample.K ...
s showed that ''ldrD'' and ''rdlD'' are both
transcribed and
primer extension
Primer extension is a technique whereby the 5' ends of RNA can be mapped - that is, they can be sequenced and properly identified.
Primer extension can be used to determine the start site of transcription (the end site cannot be determined by th ...
analysis showed the rdlD transcript is not
translated
Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...
.
Homologues exist in related
Enterobacteriaceae
Enterobacteriaceae is a large family (biology), family of Gram-negative bacteria. It was first proposed by Rahn in 1936, and now includes over 30 genera and more than 100 species. Its classification above the level of family is still a subject ...
such as ''
Salmonella enterica
''Salmonella enterica'' (formerly ''Salmonella choleraesuis'') is a rod-headed, flagellate, facultative anaerobic, Gram-negative bacterium and a species of the genus ''Salmonella''. A number of its serovars are serious human pathogens.
Epidemi ...
'' and ''
Shigella boydii
''Shigella boydii'' is a Gram-negative bacterium of the genus ''Shigella''. Like other members of the genus, ''S. boydii'' is a nonmotile, nonsporeforming, rod-shaped bacterium which can cause dysentery in humans through fecal-oral contamination ...
''. The Ldr peptide genes that have been discovered are thought to have evolved from a common ancestor.
LDR sequences
Four long direct repeat (LDR) sequences were identified during
genetic sequencing Genetic Sequencing may refer to:
* DNA sequencing
* Whole genome sequencing
Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entiret ...
of a 718
kb segment of the ''E. coli''
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 ge ...
. One of these, LDR-D was studied further in order to determine the physiological function of these regions. The genes encoded by the other three LDRs, ''ldrA, ldrB and ldrC'' were confirmed to have the same activity as ''ldrD''.
Physiological effects of LdrD
The LdrD
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
causes growth inhibition, loss of cell viability, nucleoid condensation and alteration in purine metabolism when overexpressed. Once growth arrest has been achieved, it is irreversible. Another potential effect of elevated LdrD could be reduced levels of cAMP in the cell.
It inhibits both translation and transcription, which contributes significantly to reducing the
cell
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
's viability.
Suspected mechanism of inhibition
The precise mechanism by which RdlD inhibits LdrD is unknown, however it has been shown that RdlD seems to regulate LdrD expression at the post-transcriptional level. The RdlD antisense RNA does not overlap with the translational initiation region of ''ldrD'', as is common with Type 1 toxin-antitoxin systems.
See also
*
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 ...
*
Hok/sok system The hok/sok system is a postsegregational killing mechanism employed by the R1 plasmid in ''Escherichia coli''. It was the first type I toxin-antitoxin pair to be identified through characterisation of a plasmid-stabilising locus. It is a type I sy ...
*
RatA
Rata may refer to:
Biology
* Some plants of the genus ''Metrosideros'' from New Zealand, including:
** '' Metrosideros albiflora'' (Large white rātā)
** ''Metrosideros bartlettii'' (Bartlett's rātā or Cape Reinga white rātā)
** ''Metrosider ...
References
Further reading
*
*
*
External links
* {{Rfam, id=RF01813, name=rdlD antitoxin
Antisense RNA
RNA antitoxins
Toxins