Rho factor
Encyclopedia
A ρ factor is a prokaryotic
protein
involved in the termination
of transcription
.
Rho factor is an essential transcription protein in prokaryotes. In Escherichia coli
, it is a ~275 kD hexamer of identical subunits. Each subunit has an RNA-binding domain and an ATP
-hydrolysis
domain. Rho is a member of the family of ATP-dependent hexameric helicases that function by wrapping nucleic acids around a single cleft extending around the entire hexamer. Rho functions as an ancillary factor for RNA polymerase
.
There are two types of transcriptional termination in prokaryotes, factor-dependent termination and Intrinsic termination
(also called Rho-independent termination). Rho-dependent terminators account for about half of the Escherichia coli
factor-dependent terminators. Other termination factors discovered in Escherichia coli
include Tau and nusA. Rho-dependent terminators were first discovered in bacteriophage
genomes.
A Rho factor acts on an RNA substrate. Rho's key function is its helicase
activity, for which energy is provided by an RNA-dependent ATP hydrolysis. The initial binding site for Rho is an extended (~70 nucleotides, sometimes 80-100 nucleotides) single-stranded region, rich in cytosine
and poor in guanine
, called the rho utilization site or rut, in the RNA being synthesised, upstream of the actual terminator sequence. Several rho binding sequences have been discovered. No consensus is found among these, but the different sequences each seem specific, as small mutations in the sequence disrupts its function. Rho binds to RNA and then uses its ATPase
activity to provide the energy to translocate along the RNA until it reaches the RNA-DNA helical region, where it unwinds the hybrid duplex structure. RNA polymerase pauses at the termination sequence, which is because there is a specific site around 100nt away from the Rho binding site called the Rho-sensitive pause site. So, even though the RNA polymerase is about 40nt per second faster than Rho, it does not pose a problem for the Rho termination mechanism as the RNA polymerase allows Rho factor to catch up.
In short, Rho factor acts as an ATP-dependent unwinding enzyme, moving along the newly forming RNA molecule towards its 3' end and unwinding it from the DNA template as it proceeds.
A nonsense mutation
in one gene of an operon
prevents the translation of subsequent genes in the unit. This effect is called mutational polarity. A common cause is the absence of the mRNA
corresponding to the subsequent (distal) parts of the unit. Suppose that there are Rho-dependent terminators within the transcription unit, that is, before the terminator that usually is used. Normally these earlier terminators are not used, because the ribosome
prevents Rho from reaching RNA polymerase. But a nonsense mutation releases the ribosome, so that Rho is free to attach to and/or move along the RNA, enabling it to act on RNA polymerase at the terminator. As a result, the enzyme is released, and the distal regions of the transcription unit are never transcribed.
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...
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...
involved in the termination
Termination factor
Termination is part of the process of transcribing RNA. In eukaryotes, a termination factor is required to release the newly made RNA from the transcription complex...
of transcription
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...
.
Rho factor is an essential transcription protein in prokaryotes. 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...
, it is a ~275 kD hexamer of identical subunits. Each subunit has an RNA-binding domain and an ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
-hydrolysis
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...
domain. Rho is a member of the family of ATP-dependent hexameric helicases that function by wrapping nucleic acids around a single cleft extending around the entire hexamer. Rho functions as an ancillary factor for RNA polymerase
RNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
.
There are two types of transcriptional termination in prokaryotes, factor-dependent termination and Intrinsic termination
Intrinsic termination
Intrinsic termination is a mechanism in prokaryotes that causes mRNA transcription to be stopped. In this mechanism, the mRNA contains a sequence that can base pair with itself to form a stem-loop structure 7-20 base pairs in length that is also rich in cytosine-guanine base pairs...
(also called Rho-independent termination). Rho-dependent terminators account for about half of the 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...
factor-dependent terminators. Other termination factors 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...
include Tau and nusA. Rho-dependent terminators were first discovered in bacteriophage
Bacteriophage
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid...
genomes.
A Rho factor acts on an RNA substrate. Rho's key function is its helicase
Helicase
Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.-Function:Many cellular processes Helicases are a...
activity, for which energy is provided by an RNA-dependent ATP hydrolysis. The initial binding site for Rho is an extended (~70 nucleotides, sometimes 80-100 nucleotides) single-stranded region, rich in cytosine
Cytosine
Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine . It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached . The nucleoside of cytosine is cytidine...
and poor in guanine
Guanine
Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine . In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with...
, called the rho utilization site or rut, in the RNA being synthesised, upstream of the actual terminator sequence. Several rho binding sequences have been discovered. No consensus is found among these, but the different sequences each seem specific, as small mutations in the sequence disrupts its function. Rho binds to RNA and then uses its ATPase
ATPase
ATPases are a class of enzymes that catalyze the decomposition of adenosine triphosphate into adenosine diphosphate and a free phosphate ion. This dephosphorylation reaction releases energy, which the enzyme harnesses to drive other chemical reactions that would not otherwise occur...
activity to provide the energy to translocate along the RNA until it reaches the RNA-DNA helical region, where it unwinds the hybrid duplex structure. RNA polymerase pauses at the termination sequence, which is because there is a specific site around 100nt away from the Rho binding site called the Rho-sensitive pause site. So, even though the RNA polymerase is about 40nt per second faster than Rho, it does not pose a problem for the Rho termination mechanism as the RNA polymerase allows Rho factor to catch up.
In short, Rho factor acts as an ATP-dependent unwinding enzyme, moving along the newly forming RNA molecule towards its 3' end and unwinding it from the DNA template as it proceeds.
A nonsense mutation
Nonsense mutation
In genetics, a nonsense mutation is a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in a truncated, incomplete, and usually nonfunctional protein product. It differs from a missense mutation, which is a point mutation...
in one gene of an operon
Operon
In genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single regulatory signal or promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo trans-splicing to create...
prevents the translation of subsequent genes in the unit. This effect is called mutational polarity. A common cause is the absence of the mRNA
Messenger RNA
Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein...
corresponding to the subsequent (distal) parts of the unit. Suppose that there are Rho-dependent terminators within the transcription unit, that is, before the terminator that usually is used. Normally these earlier terminators are not used, because the ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
prevents Rho from reaching RNA polymerase. But a nonsense mutation releases the ribosome, so that Rho is free to attach to and/or move along the RNA, enabling it to act on RNA polymerase at the terminator. As a result, the enzyme is released, and the distal regions of the transcription unit are never transcribed.