The EIF4E gene spans >50 kbp and contains 8 exons, one of them being alternative. It codes for the major, 4749 nucleotides long transcript variant 1, that codes 217 aa long protein. The longest transcript, variant 2 (4842 nucleotides) contains an additional in-frame exon in 3 coding region compared to variant 1 and codes for a protein (248 aa long, isoform 2) with a longer c-terminus compared to isoform 1. Transcript variant 3 is 3406 nucleotide long and uses an alternative exon for the 5UTR and 5 coding region that results in translation initiation from a distinct ATG, and an isoform 3, (237 aa) with a longer and distinct N-terminus compared to isoform 1. Transcript variants 2 and 3 are predicted from cDNA sequences, but their expression at mRNA or protein levels was not studied.

The promoter of the EIF4E gene lacks a canonical TATA box, but it contains a polypyrimidine element at position -25, named the eIF4E basal element (4EBE) that binds hnRNPK. hnRNPK interacts with TATA-binding protein and recruits it to the promoter, explaining how the 4EBE might replace the TATA box in the EIF4E promoter (Lynch et al., 2005). Mapping of the minimal EIF4E promoter was found to contain CACGTG E box repeats (positions -77 and -232) that are c-myc responsive (Jones et al., 1996; Makhlouf et al., 2001). The same elements overlap for USF binding. Later mapping studies of the 2 kb promoter found AP-1 binding elements involved in EIF4E transcriptional regulation in cardiac muscle cells (Makhlouf et al., 2001) as well as Rel, Myb, NF-kB, SP-1, NF1, STAT, AP-4, ATB and CREB consensus motifs. p53 could also be involved in the regulation of eIF4E-1 expression through its binding to c-myc, thereby preventing c-myc binding to the EIF4E promoter (Gao et al., 1998; Zhu et al., 2005).
It was shown that eIF4E mRNA contains an AU-rich elements in the 3UTR that is responsible for HuR-mediated binding and stabilization (Topisirovic et al., 2009b).

Two pseudogenes are mapped so far: EIF4EP1 (also known as EIF4EL2 and dJ1022P6.3), on chromosome 20 (location 20p13), (Entrez Gene ID: 1980), (Pelletier et al., 1991), and EIF4EP2 on chromosome 17 (17q21.32), (Entrez Gene ID: 100113387).
In the report by Gao et al. (1998), numerous intronless eIF4E pseudogenes were found, all containing premature in-frame stop codons.

eIF4E is a 25 kD cap-binding protein, which exists both in a free form and as part of a multiprotein complex termed eIF4F. The eIF4E protein has two distinct functions. First, the eIF4E polypeptide functions in delivering cellular mRNAs to the eIF4F complex to further facilitate ribosome loading and mRNA translation. The other subunits of eIF4F complex are: eIF4A, a 50 kD polypeptide, ATP-dependent RNA helicase that facilitates melting of the mRNA secondary structure, and eIF4G, a 220 kD scaffolding protein of this complex. Second, eIF4E functions in mRNA export (see below).
The cap-bound form of eIF4E was solved by X-ray crystallography for the human and mouse eIF4E and by NMR solution structure for the yeast homolog. It was shown that each consists of eight-stranded anti-parallel beta-sheets supported by three alpha-helices forming the palm and back of a "cupped" hand (Marcotrigiano et al., 1997; Matsuo et al., 1997; Tomoo et al., 2002). Two Trp residues (Trp56 and Trp102 for human eIF4E) located within a narrow cavity inside the concave surface, hold the guanine residue of the cap-analogue through pi-pi stacking interactions (McCoy et al., 1997; Wieczorek et al., 1997). A third Trp residue (Trp166 in human eIF4E) recognizes the presence of the N⁷-methyl group of the cap structure. NMR structure of cap-free eIF4E (apo-eIF4E) exhibits structural differences in the cap-binding site and dorsal surface relative to cap-eIF4E. Alterations in the S4-H4 loop distal to cap binding site seems to be a key in modulating conformational changes of eIF4E upon ligand binding (Volpon et al., 2006).
Although human and S. cerevisiae eIF4E counterparts have only approximately 30% sequence identity, they are functionally conserved and mammalian eIF4Es can rescue the lethality of eIF4E gene disruption in S. cerevisiae (Altmann et al., 1989; Joshi et al., 2002). Amino acid alignments of mammalian eIF4Es with eIF4Es from plants and yeast, coupled with deletion analyses from S. cerevisiae and D. rerio, reveal that the core of eIF4E represented by ~170 amino acids (from His37 to His200 in human eIF4E) is conserved in all eukaryotes and is sufficient for cap recognition and binding to eIF4G and 4E-BPs (Vasilescu et al., 1996; Robalino et al., 2004), while N- and C-termini are considerably variable both in length and sequence (suggesting that they are dispensable for translation). It is possible that N- and C-termini may be involved in the regulation of eIF4E activity or could affect the stability of the protein (Scheper et al., 2002; Gross et al., 2003). Crystallographic studies of mouse eIF4E bound to either a fragment of eIF4G or 4E-BP1 revealed that His37, Pro38, Val69, Trp73, Leu131, Glu132 and Leu135 (of human eIF4E) interact with eIF4E-binding regions of eIF4G and 4E-BPs (Marcotrigiano et al., 1999). Residues Val69 and Trp73 are found within the phylogenetically conserved part of the consensus sequence. Substitution of Trp73 of mammalian eIF4E to non-aromatic amino acid disrupts ability of eIF4E to interact with eIF4G and 4E-BPs (Ptushkina et al., 1999). Substitution of human eIF4E Val69 for a Gly results in a variant that efficiently binds 4E-BP1, but has reduced capacity to interact with eIF4G and 4E-BP2 (Vasilescu et al., 1996; Ptushkina et al., 1999).
eIF4E undergoes regulated phosphorylation at residue Ser209 (Flynn et al., 1995; Joshi et al., 1995). Mnk1 and Mnk2 are identified as kinases that phosphorylate Ser209, and they are targets for mitogen-activated extracellular signal-regulated kinase and stress/cytokine-activated p38 mitogen-activated protein kinase pathways (Waskiewicz et al., 1997; Wang et al., 1998; Waskiewicz et al., 1999; Scheper et al., 2001). Both enzymes also associate with eIF4G in vivo (Pyronnet et al., 1999; Waskiewicz et al., 1999; Scheper et al., 2001). The structural basis is still not clear as to whether phosphorylation of Ser209 substantially changes the affinity of eIF4E for the cap structure (Minich et al., 1994; Scheper et al., 2002b).
It was shown that eIF4E could be ubiquitinated and degraded in proteasome-dependent manner (Othumpangat et al., 2005; Murata et al., 2006).
Recently, it was suggested that eIF4E could be modified by SUMO1 conjugation (Xu et al., 2010).

eIF4E is ubiquitously expressed, and its presence is essential for viability of cells or whole organisms (Altmann et al., 1987). The level of expression and phosphorylation status may vary between tissues and cellular differentiation state (Mao et al., 1992; Fahrenkrug et al., 1999; Walsh et al., 2003). It was shown that eIF4E is over-expressed in many types of cancer (see below).

eIF4E is localized both in the cytoplasm and the nucleus of the cell. Up to 68% of eIF4E is found in the nucleus of cells from a wide variety of species ranging from yeast to humans (Lejbkowicz et al., 1992; Iborra et al., 2001; Strudwick et al., 2002). Localization of eIF4E can also be dynamic (Fahrenkrug et al., 1999; Strudwick et al., 2002).

In the cytoplasm, eIF4E functions in the rate limiting step of cap-dependent translation initiation (Sonenberg et al., 1998). Here, eIF4E directly binds the 7-methyl guanosine "m⁷G cap" structure found on the 5 end of mRNAs, and recruits transcripts to the ribosomes thereby increasing translational efficiency (Pestova et al., 2000; von der Haar et al., 2004). In order for translation to proceed, eIF4E must associate with other factors of the eIF4F complex (eIF4G and eIF4A), as well as the other factors such as the ribosome-bound eIF3 and the poly(A)-binding protein. Once formed, the eIF4F complex is thought to scan 5-3 from the cap, unwinding any existing secondary structure within the 5UTR region to reveal the translation initiation codon and to facilitate ribosome loading on the mRNA (Gingras et al., 1999). Importantly, eIF4E effects the translation of some mRNAs, known as eIF4E sensitive, more than other transcripts. When eIF4E is overexpressed, sensitive transcripts have a higher ribosome/mRNA ratio enabling more efficient translation (without modulating mRNA levels in the cytoplasm). Notably, sensitive mRNAs have more highly structured 5UTRs versus insensitive housekeeping mRNAs such as GAPDH or actin, which contain short, unstructured 5UTRs (Rhoads et al., 1993; Sonenberg et al., 1998; De Benedetti et al., 1999). Transcripts controlled at this level often code for proteins involved in proliferation such as c-myc, Pim 1, VEGF and ODC (Rhoads et al., 1993; Kevil et al., 1996; Rousseau et al., 1996; Hoover et al., 1997).
In the nucleus, eIF4E functions in the mRNA export of a specific subset of mRNAs, which contain a discrete 50 nucleotides element in their 3UTR known as the eIF4E sensitivity element (4E-SE) (Rousseau et al., 1996; Culjkovic et al., 2005; Culjkovic et al., 2006; Culjkovic et al., 2007). Many mRNAs sensitive to eIF4E at the export level code for proteins that promote proliferation and survival (such as cyclin D1 and ODC mRNAs). Unlike bulk mRNA export which is TAP/NXF1 dependent, eIF4E dependent mRNA export is CRM1 dependent and requires the 4E-SE and the mRNA export factor LRPPRC (Culjkovic et al., 2006; Topisirovic et al., 2009a).
Thus eIF4E can modulate gene expression at two levels: by exporting mRNAs to the cytoplasm increasing their concentration therein and by enhancing the translational efficiency of transcripts that are already in the cytoplasm. Not all transcripts are affected at both levels. Importantly, eIF4E requires its m⁷G cap binding function in order to act in either of these functions.
eIF4E activity is regulated by many proteins. One of the best-characterized regulators of eIF4E is eIF4E binding protein 1 (BP1) (Sonenberg et al., 1998; Gingras et al., 1999; Zimmer et al., 2000; Wendel et al., 2007). This protein uses a conserved eIF4E binding site to associate with eIF4E, and thereby precludes access of eIF4E to eIF4G and the rest of the translation machinery (Sonenberg et al., 1998). This binding site is defined as follows: YXXXXLPhi (where X is any residue and Phi is a hydrophobic residue). Studies suggest that BP1 increases cap affinity and thereby sequesters both eIF4E and the RNA in question from the translational machinery (von der Haar et al., 2004). Further, endogenous BP1 associates with eIF4E in both the nuclear and cytoplasmic compartments and thus likely modulates eIF4E activity at both the level of translation and mRNA export (Rong et al., 2008). Phosphorylation of 4E-BP1 leads to a reduction in its interaction with eIF4E and thereby, results in increased translational activity of eIF4E. 4E-BP1 phosphorylation is mTOR dependent (Proud, 2007). However, BP1^-/- and BP1^-/-BP2^-/- mice do not develop cancers more readily than controls (Blackshear et al., 1997; Tsukiyama-Kohara et al., 2001; Banko et al., 2006; Le Bacquer et al., 2007), highlighting the importance of redundancy of regulators in the control of eIF4E.
The vast majority of other eIF4E regulators contain the YXXXXLPhi motif like eIF4G and the BPs. These regulators include a set of over 200 homeodomain proteins that contain this motif. Some of these members are negative regulators of eIF4E, such as PRH/Hex. PRH is a nuclear protein that impedes eIF4Es mRNA export function, and its overexpression leads to the cytoplasmic re-distribution of eIF4E (Topisirovic et al., 2003a; Topisirovic et al., 2003b). Other members of this group of homeodomain containing regulators include Emx2, Otx, Engrailed 2, Hox11, Bicoid and HoxA9 (Topisirovic et al., 2005a). HoxA9 can stimulate both the nuclear and cytoplasmic functions of eIF4E (Topisirovic et al., 2005b).
There is also a discrete class of eIF4E regulators that utilize a RING domain to impede eIF4E function. These regulators include the promyelocytic leukemia protein PML, and arenaviral Z proteins from LCMV and Lassa viruses (Lai et al., 2000; Cohen et al., 2001; Ardley et al., 2001). Binding of PML or the Z proteins to eIF4E reduces the affinity of eIF4E for the m⁷G cap by up to 100 fold (Nathan et al., 1997; Graff et al., 2003; Topisirovic et al., 2003a). PML is a mostly nuclear protein, and thus primarily inhibits the mRNA export activity of eIF4E (Cohen et al., 2001; Kentsis et al., 2001; Culjkovic et al., 2005; Culjkovic et al., 2006; Culjkovic et al., 2008).
In conclusion, the regulation of eIF4E activity is redundant and multi-factorial. There are tissue specific regulators such as the homeodomain proteins and more ubiquitous regulators such as PML and 4E-BP1. Redundancy of regulators is seen for both the nuclear and cytoplasmic arms of eIF4E activity.

By analysis of expressed sequence tag sequences, two additional eIF4E-family members in mammals named eIF4E-2 (also known as 4EHP, 4E-LP) and eIF4E-3 were identified (Joshi et al., 2004). They differ in their structural signatures, functional characteristics and expression pattern from eIF4E (eIF4E-1). Like eIF4E-1, eIF4E-2 is expressed in all tissues, with highest levels in the testis, while eIF4E-3 is detectable only in muscles, spleen and lung. Unlike eIF4E-1, eIF4E-2 and eIF4E-3 are not able to rescue the growth of S. cerevisiae lacking a functional EIF4E gene. While both, eIF4E-2 and eIF4E-3 can bind the cap in vitro, eIF4E-2 and eIF4E-3 differ from eIF4E-1 and between each-other in their affinities to 4E-BPs and eIF4G. It is proposed that each eIF4E-family member fills a specialized role in the regulation of recruitment of mRNAs to ribosomes through differences in their ability to bind the cap and/or to interact with eIF4G and 4E-BPs.

Autism

Genome wide linkage studies in autism patients have shown linkage to the region containing the EIF4E locus on chromosome 4q (Yonan et al., 2003; Schellenberg et al., 2006). Recently, de novo chromosome translocation between 4q and 5q was reported in a boy with classic autism, and a breakpoint site was mapped within a proposed alternative transcript of eIF4E (Neves-Pereira et al., 2009). In the same study, screening of 120 autism families, two unrelated families were found, where in each case both autistic siblings and one of the parents harbored the same single nucleotide insertion at position -25 in the basal element of the EIF4E promoter. EMSA assays and reporter gene studies show that this mutation enhances EIF4E promoter activity by two fold.