An exon junction complex (EJC) is a
protein complex
A protein complex or multiprotein complex is a group of two or more associated polypeptide chains. Protein complexes are distinct from multienzyme complexes, in which multiple catalytic domains are found in a single polypeptide chain.
Protein c ...
which forms on a
pre-messenger RNA strand at the junction of two
exon
An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term ''exon'' refers to both the DNA sequence within a gene and to the corresponding sequen ...
s which have been joined together during
RNA splicing
RNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). It works by removing all the introns (non-coding regions of RNA) and ''splicing'' b ...
. The EJC has major influences on
translation
Translation is the communication of the Meaning (linguistic), meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The ...
,
surveillance
Surveillance is the monitoring of behavior, many activities, or information for the purpose of information gathering, influencing, managing or directing. This can include observation from a distance by means of electronic equipment, such as c ...
and localization of the spliced
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 ...
.
It is first deposited onto mRNA during splicing and is then transported into the
cytoplasm
In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The ...
. There it plays a major role in post-transcriptional regulation of mRNA. It is believed that exon junction complexes provide a position-specific memory of the splicing event. The EJC consists of a stable heterotetramer core, which serves as a binding platform for other factors necessary for the mRNA pathway.
[ The core of the EJC contains the ]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 ...
eukaryotic
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
initiation factor Initiation factors are proteins that bind to the small subunit of the ribosome during the initiation of translation, a part of protein biosynthesis.
Initiation factors can interact with repressors to slow down or prevent translation. They have t ...
4A-III ( eIF4A-III; a DEAD-box RNA
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
helicase
Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separatin ...
) bound to an adenosine triphosphate ( ATP) analog, as well as the additional proteins Magoh
Protein mago nashi homolog is a protein that in humans is encoded by the ''MAGOH'' gene.
Drosophila that have mutations in their mago nashi (grandchildless) gene produce progeny with defects in germplasm assembly and germline development. This ge ...
and Y14. The binding of these proteins to nuclear speckled domains has been measured recently and it may be regulated by PI3K/AKT/mTOR signaling pathways. In order for the binding of the complex to the mRNA to occur, the eIF4AIII factor is inhibited, stopping the hydrolysis of ATP.[ This recognizes EJC as an ATP dependent complex. EJC also interacts with a large number of additional proteins; most notably SR proteins.] These interactions are suggested to be important for mRNA compaction. The role of EJC in mRNA export is controversial.
Protein components
The EJC is made up of several key protein components: RNPS1
RNA-binding protein with serine-rich domain 1 is a protein that in humans is encoded by the ''RNPS1'' gene.
Function
This gene encodes a protein that is part of a post-splicing multiprotein complex, the exon junction complex, involved in both ...
, Y14, SRm160
Serine/arginine repetitive matrix protein 1 is a protein that in humans is encoded by the ''SRRM1'' gene.
Interactions
SRRM1 has been shown to interact with CDC5L
Cell division cycle 5-like protein is a protein that in humans is encoded by t ...
, Aly/REF and Magoh, among others. RNPS1 can function as a coactivator
A coactivator is a type of transcriptional coregulator that binds to an activator (a transcription factor) to increase the rate of transcription of a gene or set of genes. The activator contains a DNA binding domain that binds either to a DNA p ...
of splicing, but along with Y14, it also takes part in the process of nonsense-mediated decay
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that exists in all eukaryotes. Its main function is to reduce errors in gene expression by eliminating mRNA transcripts that contain premature stop codons. Translation of these aberrant ...
in eukaryotes. SRm160 is another coactivator that has been proposed to enhance mRNA 3’ end processing. The protein component Magoh is thought to facilitate the subcytoplasmic localization of mRNAs while Aly is engaged in nuclear mRNA export. Aly is believed to be recruited to the exon junction complex by the protein UAP56
Spliceosome RNA helicase BAT1 is an enzyme that in humans is encoded by the ''BAT1'' gene.
This gene encodes a member of the DEAD box family of RNA-dependent ATPases that mediate ATP hydrolysis during pre-mRNA splicing. The encoded protein is a ...
. UAP56 is recognized as an RNA helicase but acts as a splicing factor required for early spliceosome assembly. Another factor involved in the EJC pathway is DEK. This component is known to take part in a variety of functions ranging from splicing to transcriptional regulation and chromatin
Chromatin is a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important roles in r ...
structure.
Structure
The crystallization
Crystallization is the process by which solid forms, where the atoms or molecules are highly organized into a structure known as a crystal. Some ways by which crystals form are precipitating from a solution, freezing, or more rarely deposi ...
of the exon junction complex has revealed the structural organization of its protein components. The core of the complex is elongated with an overall dimension of 99Å by 67Å by 54Å. It is organized around the eIF4AIII factor. The factor itself consists of two different types of conformations around the mRNA: closed and open. In a closed state, the two domains of eIF4AIII form composite binding sites for the 5'-adenylyl-β,γ-imidodiphosphate (ADPNP) and mRNA.[ In the open conformation, the two domains are rotated by 160 degrees relative to closed state18. The protein components Magoh and Y14 bind together to form a heterodimer located at the 5’ pole of the EJC.] Magoh binds to an eIF4AIII domain through interactions between residues from its two C-terminal helices and one end of a large β-sheet
The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a gen ...
.[ Conserved residues in the linker between the two eIF4AIII domains form ]salt bridge
In electrochemistry, a salt bridge or ion bridge is a laboratory device used to connect the oxidation and reduction half-cells of a galvanic cell (voltaic cell), a type of electrochemical cell. It maintains electrical neutrality within the in ...
s or hydrogen bonds with specific residues in Magoh.[ Other bonding occurs between the second loop of the Magoh β–sheet and the two eIF4AIII domains and their linker.][ There is only a single partial bond formed between Y14 and eIF4AIII. This consists of a salt bridge between the conserved residues Y14 Arg108 and eIF4AIII Asp401.][ If mutations were to occur to both of these residues, association of Magoh-Y14 with EJC would be non-existent.]
Mechanism
During the second step of splicing in eukaryotic cells, the EJC is deposited approximately 20-24 nucleotides
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 w ...
from the 5’ end upstream of the splice junction (where two exons are joined), when the lariat has formed and the exons are ligated together. The binding of the EJC to the mRNA occurs in a sequence independent manner, to form the mature messenger ribonucleoprotein
Nucleoproteins are proteins conjugated with nucleic acids (either DNA or RNA). Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins.
Structures
Nucleoproteins tend to be positively charged, facilitating in ...
(mRNP). The EJC remains stably bound to this mRNP as it is exported out of the nucleus and into the cytoplasm. Protein components are either bound to or released by the EJC as it is transported. In order for the translocation of mRNAs through the nuclear pore complex to occur, a heterodimer consisting of NXF1
Nuclear RNA export factor 1, also known as NXF1 or TAP, is a protein which in humans is encoded by the ''NXF1'' gene.
Function
This gene is one member of a family of nuclear RNA export factor genes. Common domain features of this family are a no ...
/TAP and NXT1
NTF2-related export protein 1 is a protein that in humans is encoded by the ''NXT1'' gene
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation' ...
/ p15 must bind to the transcripts. NXF1/TAP is a major receptor for the export of mRNAs to the cytoplasm. This is because it interacts with both RNA-binding adapter proteins and components of the nuclear pore
A nuclear pore is a part of a large complex of proteins, known as a nuclear pore complex that spans the nuclear envelope, which is the double membrane surrounding the eukaryotic cell nucleus. There are approximately 1,000 nuclear pore complexes ...
complex.
Recognition of a premature termination codon occurs during translation in the cytoplasm. The image shown below implies that this event is nuclear, contrary to the general view in this field. Readers should be aware that translation in the nucleus is a highly controversial subject that is not well-supported by data.
In nonsense mediated decay
Exon junction complexes play a major role in mRNA surveillance
mRNA surveillance mechanisms are pathways utilized by organisms to ensure fidelity and quality of messenger RNA (mRNA) molecules. There are a number of surveillance mechanisms present within cells. These mechanisms function at various steps of th ...
. More specifically, they are found in the nonsense mediated decay
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that exists in all eukaryotes. Its main function is to reduce errors in gene expression by eliminating mRNA transcripts that contain premature stop codons. Translation of these aberrant ...
pathway (NMD), wherein mRNA transcripts with premature stop codons are degraded. In normal mRNA translation, the ribosome
Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to ...
binds to the transcript and begins 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 ...
chain elongation. It continues on until it reaches the location of the exon junction complex, which it then displaces. Next, translation is complete when the ribosome reaches a termination codon
In molecular biology (specifically protein biosynthesis), a stop codon (or termination codon) is a codon (nucleotide triplet within messenger RNA) that signals the termination of the translation process of the current protein. Most codons in mess ...
. In NMD, the mRNA transcript contains a premature termination codon (PTC) due to a 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 leading to a truncated, incomplete, and usually nonfunctional protein produc ...
. If this codon occurs prior to the EJC site, the EJC will remain bound, triggering mRNA decay. The EJC and its position serve as a type of regulator, determining whether the transcript is defective or not.
EJCs are also known to take part in NMD in another way; the recruitment of the surveillance factors UPF1
Regulator of nonsense transcripts 1 is a protein that in humans is encoded by the ''UPF1'' gene.
Function
This gene encodes a protein that is part of a post-splicing multiprotein complex, the exon junction complex, involved in both mRNA nuclea ...
, UPF2
Regulator of nonsense transcripts 2 is a protein that in humans is encoded by the ''UPF2'' gene.
Function
This gene encodes a protein that is part of a post-splicing multiprotein complex, the exon junction complex, involved in both mRNA nuclea ...
and UPF3. These proteins are the most important components of the NMD mechanism. The EJC protein MAGOH, Y14 and eIF4AIII provide a binding for UPF3, which acts as a bridge between UPF2 and UPF1 forming a trimeric complex.
Within this complex, UPF2 and UPF3 act cooperatively to promote ATPase
ATPases (, Adenosine 5'-TriPhosphatase, adenylpyrophosphatase, ATP monophosphatase, triphosphatase, SV40 T-antigen, ATP hydrolase, complex V (mitochondrial electron transport), (Ca2+ + Mg2+)-ATPase, HCO3−-ATPase, adenosine triphosphatase) are ...
and RNA helicase of UPF1.[ The EJC core stably anchors the UPF complex to the mRNA, and aids in regulation of essential UPF1 protein.][ Ribosomes which are stalled on a PTC recruit UPF1 through interactions with the release factor ]eRF1
Eukaryotic translation termination factor 1 (eRF1), also known as TB3-1, is a protein that in humans is encoded by the ''ETF1'' gene.
In eukaryotes and archaea, this is the sole class 1 release factor (eRF) which recognizes all three stop codon ...
and eRF3.[ Along with the protein ]SMG1
Serine/threonine-protein kinase SMG1 is an enzyme that in humans is encoded by the ''SMG1'' gene. SMG1 belongs to the phosphatidylinositol 3-kinase-related kinase protein family.
Function
This gene encodes a protein involved in nonsense-medi ...
, eRF1, eRF3 and UPF1 form the complex SURF. This complex forms a bridge between the ribosome and the downstream EJC which is associated with UPF3 and UPF2.[ This interaction triggers the ]phosphorylation
In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...
of UPF1 by SMG1, causing the dissociation of eRF1 and eRF3.[ The complex produced consists of EJC, UPF3, UPF2, phosphorylated UPF1 and SMG1 and in turn triggers degradation of the mRNA.][
]
Notes and references
{{reflist
RNA
Spliceosome