AdoCbl riboswitch
Encyclopedia
AdoCbl riboswitch is a cis-regulatory riboswitch
element present in untranslated regions of mRNA where binding adenosylcobalamin (AdoCbl) causes a change in gene expression
. This riboswitch has been shown to be conserved across several strains of bacteria
and has an influence over the expression of the ethanolamine
utilization genes. Its is proposed to be a subclass of the previously described classical AdoCbl-sensing riboswitch.
Ethanolamine is abundant in the human intestinal tract as it is the product of the breakdown of the phosphatidylethanolamine from cell membranes and is also present in processed food. Most bacteria
that inhabit the intestinal tract can utilize ethanolamine as a carbon
and nitrogen
source by upregulating the expression of the ethanolamine utilization genes
; This may have a survival advantage.
The expression of the ethanolamine utilization genes (eutG) is influenced by two different mechanisms. The first is a two component regulatory system that senses the presence of ethanolamine and the second mechanism is a AdoCbl riboswitch that senses the presence of AdoCbl, a cofactor
needed for the breakdown of ethanolamine. A study showed that both these regulatory elements need to be activated for the bacteria to grow efficiently on medium containing ethanolamine. Bioinformatic
studies were initially unsuccessful in identifying AdoCbl riboswitches within the bacteria genomes
, but subsequent studies of the intergenic regions of the eutG locus using Ribex identified an RNA
element between the eutT and eutG genes.
This new subclass of AdoCbl riboswitches has both sequence and structural
conservation with the core region of the classical AdoCbl-sensing riboswitches however it has some clear differences. The new element lacks a paired region
formed by the pairing of the 5'3'
ends found in canonical AdoCbl riboswitches. It also has an additional extra base-paired region near the 3′ terminus that is absent from the classical AdoCbl riboswitches..
In line probing
analysis of this new riboswitch showed that the presence of AdoCbl increased mRNA stability and causes a global conformational change
in the riboswitch. This riboswitch unlike previously characterized AdoCbl riboswitches is thought to inhibit transcription
termination
as transcription terminator helices have been identified downstream of the riboswitch. This suggests that unlike characterized AdoCbl riboswitches that usually inhibit cobalamin biosythesis by promoting transcription termination this newly identified AdoCbl riboswitch promotes the expression of downstream genes.
Riboswitch
In molecular biology, a riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the gene's activity. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the...
element present in untranslated regions of mRNA where binding adenosylcobalamin (AdoCbl) causes a change in gene expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
. This riboswitch has been shown to be conserved across several strains of bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
and has an influence over the expression of the ethanolamine
Ethanolamine
Ethanolamine, also called 2-aminoethanol or monoethanolamine , is an organic chemical compound that is both a primary amine and a primary alcohol . Like other amines, monoethanolamine acts as a weak base...
utilization genes. Its is proposed to be a subclass of the previously described classical AdoCbl-sensing riboswitch.
Ethanolamine is abundant in the human intestinal tract as it is the product of the breakdown of the phosphatidylethanolamine from cell membranes and is also present in processed food. Most bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
that inhabit the intestinal tract can utilize ethanolamine as a carbon
Carbon
Carbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds...
and nitrogen
Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
source by upregulating the expression of the ethanolamine utilization genes
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
; This may have a survival advantage.
The expression of the ethanolamine utilization genes (eutG) is influenced by two different mechanisms. The first is a two component regulatory system that senses the presence of ethanolamine and the second mechanism is a AdoCbl riboswitch that senses the presence of AdoCbl, a cofactor
Cofactor (biochemistry)
A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes, and cofactors can be considered "helper molecules" that assist in biochemical transformations....
needed for the breakdown of ethanolamine. A study showed that both these regulatory elements need to be activated for the bacteria to grow efficiently on medium containing ethanolamine. Bioinformatic
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
studies were initially unsuccessful in identifying AdoCbl riboswitches within the bacteria genomes
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....
, but subsequent studies of the intergenic regions of the eutG locus using Ribex identified an RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
element between the eutT and eutG genes.
This new subclass of AdoCbl riboswitches has both sequence and structural
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
conservation with the core region of the classical AdoCbl-sensing riboswitches however it has some clear differences. The new element lacks a paired region
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
formed by the pairing of the 5'3'
Directionality (molecular biology)
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 5′-end and a 3′-end...
ends found in canonical AdoCbl riboswitches. It also has an additional extra base-paired region near the 3′ terminus that is absent from the classical AdoCbl riboswitches..
In line probing
RNA structure probing
Structure probing of nucleic acids is the process by which biochemical techniques are used to determine nucleic acid structure. This analysis can be used to define the patterns which can infer the molecular structure, experimental analysis of molecular structure and function, and further...
analysis of this new riboswitch showed that the presence of AdoCbl increased mRNA stability and causes a global conformational change
Conformational change
A macromolecule is usually flexible and dynamic. It can change its shape in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a conformational change...
in the riboswitch. This riboswitch unlike previously characterized AdoCbl riboswitches is thought to inhibit 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...
termination
Termination
Termination may refer to:In science:*Termination codon, in molecular biology*Termination factor, in genetics, part of the process of transcribing RNA...
as transcription terminator helices have been identified downstream of the riboswitch. This suggests that unlike characterized AdoCbl riboswitches that usually inhibit cobalamin biosythesis by promoting transcription termination this newly identified AdoCbl riboswitch promotes the expression of downstream genes.