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Eukaryotic initiation factor 4A-I (also known as eIF4A1 or DDX2A) is a 46 kDa
cytosolic The cytosol, also known as cytoplasmic matrix or groundplasm, is one of the liquids found inside cells ( intracellular fluid (ICF)). It is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondri ...
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
that, in humans, is encoded by the ''EIF4A1''
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
, which is located on
chromosome A chromosome is a package of DNA containing part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with nucleosome-forming packaging proteins; in eukaryotic cells, the most import ...
17. It is the most prevalent member of the
eIF4A The eukaryotic initiation factor-4A (eIF4A) family consists of 3 closely related proteins EIF4A1, EIF4A2, and EIF4A3. These factors are required for the binding of Messenger RNA, mRNA to 40S ribosome, ribosomal subunits. In addition these prot ...
family Family (from ) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). It forms the basis for social order. Ideally, families offer predictabili ...
of ATP-dependant RNA helicases, and plays a critical role in the initiation of cap-dependent eukaryotic protein translation as a component of the
eIF4F Eukaryotic initiation factor 4F (eIF4F) is a heterotrimeric protein complex that binds the Five-prime cap, 5' cap of Messenger RNA, messenger RNAs (mRNAs) to promote eukaryotic translation initiation. The eIF4F complex is composed of three non-i ...
translation initiation complex. eIF4A1 unwinds the secondary structure of RNA within the 5'-UTR of
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 ...
, a critical step necessary for the recruitment of the 43S preinitiation complex, and thus the translation of protein in
eukaryotes The eukaryotes ( ) constitute the domain of Eukaryota or Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of ...
. It was first characterized in 1982 by Grifo, ''et al.'', who purified it from
rabbit Rabbits are small mammals in the family Leporidae (which also includes the hares), which is in the order Lagomorpha (which also includes pikas). They are familiar throughout the world as a small herbivore, a prey animal, a domesticated ...
reticulocyte In hematology, reticulocytes are immature red blood cells (RBCs). In the process of erythropoiesis (red blood cell formation), reticulocytes develop and mature in the bone marrow and then circulate for about a day in the blood stream before dev ...
lysate.


Background

The regulation of the
translation Translation is the communication of the semantics, 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 English la ...
of mRNA transcripts into protein is one of the best ways that a cell can alter its response to its environment, as changes to the transcription of genes often takes considerably more time to be enacted. Protein translation can be broken into four phases: activation, initiation, elongation, and termination. Of these steps, initiation is the one for which cells have the most control. It is the rate limiting step of protein synthesis, controlled by a myriad of proteins known as the eukaryotic initiation factors, or eIFs. Relative abundance of these factors or their relative individual activities afford eukaryotic cells broad control over the rate of initiation and thus protein synthesis. eIFs are regulated under well known intracellular signalling pathways, such as the
PI3K/AKT/mTOR pathway The PI3K/AKT/mTOR pathway is an intracellular signaling pathway important in regulating the cell cycle. Therefore, it is directly related to cellular quiescence, proliferation, cancer, and longevity. PI3K activation phosphorylates and activates ...
, however other biochemical layers of regulation, such as the complexity of RNA secondary structure in the 5′-UTR, are becoming evident with further research. The eIF4A subfamily in mammals is made up of three
paralogs Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speci ...
, eIF4A1, eIF4A2, and eIF4A3. eIF4A1 and eIF4A2 share 90% sequence similarity, and are both cytoplasmic proteins, while eIF4A3 is localized to the
nucleus Nucleus (: nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucleu ...
, and shares only 60% homology. Historically, eIF4A1 and eIF4A2 were considered interchangeable, due to this being observed in ''
in vitro ''In vitro'' (meaning ''in glass'', or ''in the glass'') Research, studies are performed with Cell (biology), cells or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in ...
'' experiments, but further investigation has shown that eIF4A1 is more prevalent in dividing cells while eIF4A2 is more abundant in non-dividing cells, and furthermore, more recent evidence suggests that they might have functionally distinct roles ''
in vivo Studies that are ''in vivo'' (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, an ...
''.


Structure

eIF4A1 is a member of the
DEAD box DEAD box proteins are involved in an assortment of metabolic processes that typically involve RNAs, but in some cases also other nucleic acids. They are highly conserved in nine motifs and can be found in most prokaryotes and eukaryotes, but not ...
family of RNA helicases. RNA helicases are enzymes that use the energy released from the hydrolysis of ATP to manipulate the secondary structure of RNA, and the DEAD box family is the largest family of RNA helicases. The name "DEAD box" refers the key D-E-A-D amino acid sequence on motif II of the helicase that participates in
nucleoside triphosphate A nucleoside triphosphate is a nucleoside containing a nitrogenous base bound to a 5-carbon sugar (either ribose or deoxyribose), with three phosphate groups bound to the sugar. They are the molecular precursors of both DNA and RNA, which are chai ...
binding (in the instance of eIF4A1, ATP). Other conserved motifs, shared by all eIF4A family proteins, are the Q, I, Ia, Ib, III, IV, V and VI motifs. Motifs Ia, Ib, IV and V bind RNA, motifs I, II, and III mediate RNA-dependent
ATPase ATPases (, Adenosine 5'-TriPhosphatase, adenylpyrophosphatase, ATP monophosphatase, triphosphatase, ATP hydrolase, adenosine triphosphatase) are a class of enzymes that catalyze the decomposition of ATP into ADP and a free phosphate ion or ...
activity, and motif VI, is required for both RNA binding and ATP hydrolysis. The DEAD box family is marked by a structurally highly conserved helicase core consisting of two
RecA RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA in bacteria. Structural and functional homologs to RecA have been found in all kingdoms of life. RecA serves as an archetype for this class of homologous DNA repair p ...
-like domains joined by a flexible hinge region around which the protein can open and close upon hydrolysis of ATP. The cleft formed between these two domains forms the ATP-binding pocket. The RNA molecule binds opposite to this binding pocket, stretching across each of the domains. This core is flanked by variable auxiliary domains, which confer the unique function of each RNA helicase to them partly by allowing for specific binding to accessory proteins.


Function

eIF4A1 is an ATP-dependent RNA helicase, however the exact nature of its dependence on ATP for its function is still debated. Although after ATP binding, the subsequent hydrolysis induces conformational changes in eIF4A1, other DEAD-box RNA helicases have been shown to possess helicase activity in the presence of nonhydrolyzable analogues of ATP, suggesting that binding, and not hydrolysis, is the more important element in regulating activity. eIF4A1 is a component of the eIF4F translation initiation complex, along with
eIF4E Eukaryotic translation initiation factor 4E, also known as eIF4E, is a protein in humans encoded by the ''EIF4E'' gene. eIF4E plays a central role in translation initiation and is involved in regulating protein synthesis. Its activity influences ...
, the 5'-terminal cap binding protein, and
eIF4G Eukaryotic translation initiation factor 4 G (eIF4G) is a protein involved in eukaryotic translation initiation and is a component of the eIF4F cap-binding complex. Orthologs of eIF4G have been studied in multiple species, including humans, yeast ...
, the scaffold protein that holds eIF4A and eIF4E together. The eIF4F complex is often accompanied by the accessory proteins eIF4B and eIF4H, either of which can differentially enhance the activity of eIF4A1. After mRNA is transcribed from DNA and translocated to the cytoplasm, and the cytosolic PABP is bound to the Poly(A)-tail of the nascent mRNA, its 5'-cap will bind to eIF4E and PABP will bind to eIF4G. eIF4A1 will then unwind the RNA secondary structure from 5' to 3' as the 43S PIC is recruited to the eIF4F complex. The 43S PIC will scan the unwound mRNA from 5' to 3' as well, until it reaches the AUG
start codon The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and archaea and a ''N''-formylmethionine (fMet) in bacteria, mitochondria and plastids. ...
, whereupon the 60S ribosomal subunit will be recruited to begin the process of elongation.


Regulation

The transcription of eIF4A1 is driven by the
transcription factor In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription (genetics), transcription of genetics, genetic information from DNA to messenger RNA, by binding t ...
MYC ''Myc'' is a family of regulator genes and proto-oncogenes that code for transcription factors. The ''Myc'' family consists of three related human genes: ''c-myc'' ( MYC), ''l-myc'' ( MYCL), and ''n-myc'' ( MYCN). ''c-myc'' (also sometimes r ...
. On its own, the helicase activity of eIF4A1 is poor, however this feature imposes a practical restraint on eIF4A1, as nonspecific, "unintended," helicase activity in the cell would be detrimental to the function of certain endogenous, necessary RNA structures. Its effectiveness considerably improves in the presence of eIF4B and eIF4H, binding partners that modulate its activity. When eIF4B binds to eIF4A1, the helicase activity of eIF4A1 is increased over 100-fold, but when eIF4H binds instead, the increase is not nearly as great, suggesting different relative concentrations of these accessory proteins may confer a further level of regulation of the efficiency of eIF4A1. Conversely, eIF4A1 activity is suppressed when it is bound to PDCD4, a
tumor suppressor A tumor suppressor gene (TSG), or anti-oncogene, is a gene that regulates a cell (biology), cell during cell division and replication. If the cell grows uncontrollably, it will result in cancer. When a tumor suppressor gene is mutated, it results ...
itself modulated by
mTOR The mammalian target of rapamycin (mTOR), also referred to as the mechanistic target of rapamycin, and sometimes called FK506-binding protein 12-rapamycin-associated protein 1 (FRAP1), is a kinase that in humans is encoded by the ''MTOR'' gene. ...
and ''miR-21''. PCDC4 is typically localized to the nucleus in healthy cells, however, under carcinogenic conditions, it translocates to the nucleus and two separate eIF4A1 molecules will bind to it, inhibiting the ability of eIF4A1 to bind to RNA by locking the molecules into their inactive conformation, thereby preventing binding to eIF4G.


Role in Disease


Cancer

Translational dysregulation is a hallmark of
malignant transformation Malignant transformation is the process by which cells acquire the properties of cancer. This may occur as a primary process in normal tissue, or secondarily as ''malignant degeneration'' of a previously existing benign tumor. Causes There are ...
of
cancer Cancer is a group of diseases involving Cell growth#Disorders, abnormal cell growth with the potential to Invasion (cancer), invade or Metastasis, spread to other parts of the body. These contrast with benign tumors, which do not spread. Po ...
cells. Cancer cells in growing tumors become "addicted" to heightened levels of protein translation, and particularly dependent on up-regulated translation of pro-oncogenic mRNAs. These pro-oncogenic mRNAs have characteristically longer 5'-UTRs with more complex secondary structures, and up-regulation of eIF4A1 has been implicated in several human cancers (See Table). Given the general trend of eIF4A1 overexpression driving cancer, there is interest in developing inhibitors for the enzyme. Several natural compounds have been identified as candidate inhibitors for development, though they inhibit both eIF4A1 and eIF4A2 non-specifically. These include hippuristanol, silvestrol and pateamine A, among others. Silvestrol, in particular is a rocaglate derivative, and this class of compounds could be viable eIF4A inhibitors.


Viral Infections

Viruses A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are found in almo ...
rely on hijacking the cellular machinery of the cells they infect to create their own viral proteins and allow them to continue infecting new cells. Their ability to manipulate eIFs like eIF4A1, therefore, considerably impacts their
virulence Virulence is a pathogen's or microorganism's ability to cause damage to a host. In most cases, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host. The pathogenicity of an organism—its abili ...
. For instance,
cytomegalovirus ''Cytomegalovirus'' (CMV) (from ''cyto-'' 'cell' via Greek - 'container' + 'big, megalo-' + -''virus'' via Latin 'poison') is a genus of viruses in the order '' Herpesvirales'', in the family '' Herpesviridae'', in the subfamily '' Betaherp ...
relies on eIF4A to drive its protein synthesis. The viral protein pUL69 stabilizes the formation of eIF4F, through binding to eIF4A, a process by which eIF4E is prevented from dissociating from the eIF4F complex. eIF4E, thus, is no longer able to be sequestered by its negative regulator, 4EBP. Furthermore, cytomegalovirus stimulates the synthesis of all elements of the eIF4F complex in order to drive protein synthesis. Other viruses, like '' Cotesia plutellae''
bracovirus ''Bracovirus'' is a genus of viruses, in the family ''Polydnaviridae''. Bracoviruses are an ancient symbiotic virus contained in parasitic braconid wasps that evolved from the '' nudivirus'' approximately 190 million years ago and has been evol ...
(CpBV), that favor cap-independent translation, will take advantage of eIF4A1 in the reverse context, by sequestering eIF4A1 away from the eIF4F complex with viral binding partners, in this case a protein called CpBV15β, thus inhibiting endogenous cap-dependent mRNA translation and favoring viral protein translation. The compounds mentioned in the above section about cancer, hippuristanol, silvestrol, pateamine A, rocaglate derivatives, etc., could also be applied as putative viral inhibitors.


References


Further reading

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External links


pUL69 of cytomegalovirus
(UniProt)
CpBV15β of Cotesia plutellae bracovirus
(UniProt) {{PDB Gallery, geneid=1973