RdlD RNA is a family of small non-coding RNA

Non-coding RNA

A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...

s which repress the protein LdrD in a 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...

. It was discovered in Escherichia 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...

strain K-12 in a long direct repeat

Tandem repeat

Tandem repeats occur in DNA when a pattern of two or more nucleotides is repeated and the repetitions are directly adjacent to each other. -Example:An example would be:in which the sequence A-T-T-C-G is repeated three times.-Terminology:...

 (LDR) named LDR-D. This locus

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...

 encodes two products: a 35 amino acid

Amino acid

Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...

 peptide toxin (ldrD) and a 60 nucleotide

Nucleotide

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...

 RNA antitoxin. The 374nt toxin mRNA has a half-life

Half-life

Half-life, abbreviated t½, is the period of time it takes for the amount of a substance undergoing decay to decrease by half. The name was originally used to describe a characteristic of unstable atoms , but it may apply to any quantity which follows a set-rate decay.The original term, dating to...

 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

Northern blot

The northern blot is a technique used in molecular biology research to study gene expression by detection of RNA in a sample. With northern blotting it is possible to observe cellular control over structure and function by determining the particular gene expression levels during differentiation,...

s showed that ldrD and rdlD are both transcribed

Transcription (genetics)

Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...

 and primer extension

Primer extension

Primer extension is a technique whereby the 5' ends of RNA or DNA can be mapped.Primer extension can be used to determine the start site of RNA transcription for a known gene. This technique requires a radiolabelled primer which is complementary to a region near the 5' end of the gene...

 analysis showed the rdlD transcript is not translated

Translation (genetics)

In molecular biology and genetics, translation is the third stage of protein biosynthesis . In translation, messenger RNA produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein...

.

Homologues exist in related Enterobacteriaceae

Enterobacteriaceae

The Enterobacteriaceae is a large family of bacteria that includes many of the more familiar pathogens, such as Salmonella, Escherichia coli, Yersinia pestis, Klebsiella and Shigella. This family is the only representative in the order Enterobacteriales of the class Gammaproteobacteria in the...

 such as Salmonella enterica

Salmonella enterica

Salmonella enterica is a rod-shaped flagellated, facultative anaerobic, Gram-negative bacterium, and a member of the genus Salmonella.- Epidemiology :...

and Shigella boydii

Shigella boydii

Shigella boydii is a Gram-negative bacteria of the genus Shigella. Like other member of the genus, S. boydii is a non-motile, non-sporeforming, rod-shaped bacteria 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

DNA sequencing

DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....

 of a 718kb segment of the E. coli genome

Genome

In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

. 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

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 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 contirbutes significantly to reducing the cell

Cell (biology)

The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....

'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.