The eukaryotic initiation factor-4A (eIF4A) family consists of 3 closely related

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 ...

EIF4A1 Eukaryotic initiation factor 4A-I (also known as eIF4A1 or DDX2A) is a 46 kDa cytosolic protein that, in humans, is encoded by the ''EIF4A1'' gene, which is located on chromosome 17. It is the most prevalent member of the eIF4A protein family, fa ...

EIF4A2 Eukaryotic initiation factor 4A-II is a protein that in humans is encoded by the ''EIF4A2'' 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 ...

, and

EIF4A3 Eukaryotic initiation factor 4A-III is a protein that in humans is encoded by the ''EIF4A3'' gene. Function This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp- Glu- Ala-Asp ...

. These factors are required for the binding 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 ...

40S The eukaryotic small ribosomal subunit (40S) is the smaller subunit of the eukaryotic 80S ribosomes, with the other major component being the large ribosomal subunit (60S). The "40S" and "60S" names originate from the convention that ribosomal p ...

ribosomal Ribosomes () are macromolecular machines, found within all cells, that perform biological protein synthesis (messenger RNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to fo ...

subunits. In addition these proteins are

helicase Helicases are a class of enzymes that are 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 double helix, separating the two hybridized ...

s that function to unwind double-stranded

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

Background

The mechanisms governing the basic subsistence of

eukaryotic cells 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 li ...

are immensely complex; it is therefore unsurprising that regulation occurs at a number of stages of

protein synthesis Protein biosynthesis, or protein synthesis, is a core biological process, occurring inside cells, balancing the loss of cellular proteins (via degradation or export) through the production of new proteins. Proteins perform a number of critica ...

– the regulation of translation has become a well-studied field. Human translational control is of increasing research interest as it has connotations in a range of diseases. Orthologs of many of the factors involved in human translation are shared by a range of eukaryotic organisms; some of which are used as model systems for the investigation of translation initiation and elongation, for example:

sea urchin Sea urchins or urchins () are echinoderms in the class (biology), class Echinoidea. About 950 species live on the seabed, inhabiting all oceans and depth zones from the intertidal zone to deep seas of . They typically have a globular body cove ...

eggs upon fertilization, rodent brain and rabbit reticulocytes. Monod and Jacob were among the first to propose that "the synthesis of individual proteins may be provoked or suppressed within a cell, under the influence of specific external agents, and the relative rates at which different proteins may be profoundly altered, depending upon external conditions". Almost half a century after the flurry of postulations arising from the revelation of the central dogma of

molecular biology Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactio ...

, of which the preceding supposition by Monod and Jacob is an example; contemporary researchers still have much to learn about the modulation of genetic expression. Synthesis of protein from

mature messenger RNA Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Unlike the eukaryotic RNA immediately after transcription ...

in eukaryotes is divided into translation initiation, elongation, and termination of these stages; the initiation of translation is the rate limiting step. Within the process of translation initiation; the bottleneck occurs shortly before the

ribosome Ribosomes () are molecular machine, macromolecular machines, found within all cell (biology), cells, that perform Translation (biology), biological protein synthesis (messenger RNA translation). Ribosomes link amino acids together in the order s ...

binds to the 5’ m7GTP facilitated by a number of proteins; it is at this stage that constrictions born of stress,

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

starvation etc. take effect.

Function

Eukaryotic initiation factor complex 2 (eIF2) forms a

ternary complex A ternary complex is a protein complex containing three different molecules that are bound together. In structural biology, ''ternary complex'' can also be used to describe a crystal containing a protein with two small molecules bound, such as a ...

with GTP and the initiator Met-

tRNA Transfer ribonucleic acid (tRNA), formerly referred to as soluble ribonucleic acid (sRNA), is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes). In a cell, it provides the physical link between the gene ...

– this process is regulated by guanine nucleotide exchange and

phosphorylation In biochemistry, phosphorylation is described as the "transfer of a phosphate group" from a donor to an acceptor. A common phosphorylating agent (phosphate donor) is ATP and a common family of acceptor are alcohols: : This equation can be writ ...

and serves as the main

regulatory element A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism. Regulation of gene expression is an essential feature of all living organisms and vir ...

of the bottleneck of

gene expression Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...

. Before translation can progress to the elongation stage, a number of initiation factors must facilitate the synergy of the ribosome and the mRNA and ensure that the 5’ UTR of the mRNA is sufficiently devoid of

secondary structure Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

. Binding in this way is facilitated by group 4 eukaryotic initiation factors;

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 ...

has implications in the normal regulation of translation as well as the transformation and progression of cancerous cells; as such, it represents an interesting field of research.

Mechanism

The repertoire of compounds involved in eukaryotic translation consists of initiation factor classes 1 – 6;

is responsible for the binding of capped mRNA to the

ribosomal subunit via

eIF3 Eukaryotic initiation factor 3 (eIF3) is a multiprotein complex that functions during the initiation phase of eukaryotic translation. It is essential for most forms of Eukaryotic translation#Cap-dependent initiation, cap-dependent and Eukaryotic ...

. The mRNA cap is bound by

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 ...

(25 kDa), eIF4G (185 kDa) acts as a scaffold for the complex whilst the ATP-dependent RNA helicase eIF4A (46 kDa) processes the secondary structure of the mRNA 5’ UTR to render it more conducive to ribosomal binding and subsequent translation. Together these three proteins are referred to as

. For maximal activity; eIF4A also requires

eIF4B Eukaryotic translation initiation factor 4B is a protein that in humans is encoded by the ''EIF4B'' gene. Interactions eIF4B has been shown to interact with and stimulate the activity of eIF4A and bind to the eIF3 complex through the eIF3A su ...

(80 kDa), which itself is enhanced by

eIF4H Eukaryotic translation initiation factor 4H is a protein that in humans is encoded by the ''EIF4H'' gene. This gene encodes one of the translation initiation factors, which function to stimulate the initiation of protein synthesis at the level of ...

(25 kDa). A study conducted by Bi ''et al.'' in

wheat germ The germ of a cereal grain is the part that develops into a plant; it is the seed embryo. Along with bran, germ is often a by-product of the milling that produces refined grain products. Cereal grains and their components, such as wheat germ ...

seemed to indicate that eIF4A has a higher binding affinity for ADP than ATP except in the presence of eIF4B, which increased the ATP binding affinity tenfold without affecting ADP affinity. Once bound to the 5’ cap of mRNA, this 48S complex then searches for the (usually) 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. ...

and translation begins.

Genes

In humans, the gene encoding eIF4A isoform I has a transcript length of 1741bp, contains 11 exons, and is located on chromosome 17. The genes for human isoforms II and III reside on chromosomes 3 and 17 respectively.

Proteins

The 407 residue, 46 kDa, protein eIF4A is the prototypical 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 ...

helicase family, so-called due to their conserved four-residue D-E-A-D sequence. This family of helicases is found in a range of prokaryotic and eukaryotic organisms including humans, wherein they catalyse a variety of processes including embryogenesis and

RNA splicing RNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre-mRNA) transcription (biology), transcript is transformed into a mature messenger RNA (Messenger RNA, mRNA). It works by removing all the introns (non-cod ...

as well as translation initiation. Crystallographic analysis of yeast eIF4A carried out by Carruthers ''et al.'' (2000) revealed that the molecule is approximately 80 Å in length and has a “dumbbell” shape where the proximal section represents an 11 residue (18 Å) linker postulated to confer a degree of flexibility and distension to the molecule in solution. eIF4A is an abundant cytoplasmic protein. Three isoforms of eIF4A exist; I and II share 95% amino acid similarity and have been found simultaneously in rabbit reticulocyte

in a ratio of 4:1, respectively. The third isoform; eIF4A III, which shares only 65% similarity to the other isoforms is believed to be a core component of the exon junction complex involved in pre-mRNA splicing.

References