Translation is the cellular process of converting genetic information from messenger RNA (mRNA) into protein. Cells primarily use a cap-dependent method to initiate translation, but an alternative pathway exists for specialized circumstances. This route is directed by an Internal Ribosome Entry Site (IRES), a sequence within an mRNA that allows protein synthesis to begin from an internal starting point.
Cap-Dependent Translation Initiation
The standard method for initiating protein synthesis in eukaryotic cells is cap-dependent translation. This process begins at the 5′ end of an mRNA molecule, which has a chemical modification called a 5′ cap. The cap recruits eukaryotic initiation factors (eIFs), including the eIF4F complex, which is composed of eIF4E, eIF4A, and eIF4G.
The eIF4E protein binds to the 5′ cap. Through its connection with the scaffolding protein eIF4G, it helps recruit the rest of the translation machinery, including the small (40S) ribosomal subunit, to the capped end of the mRNA.
Once in place, the 40S ribosomal subunit scans the mRNA until it finds the AUG start codon. The large (60S) ribosomal subunit then joins to form a complete (80S) ribosome. This event marks the end of initiation and the start of the elongation phase, where the protein is synthesized.
Mechanism of IRES-Mediated Initiation
IRES-mediated initiation allows protein synthesis to begin without the 5′ cap. This is possible because the IRES is not a simple sequence but a highly structured region within the mRNA. It folds into a specific three-dimensional shape that directly recruits the translational machinery, acting as a landing pad for the small 40S ribosomal subunit.
This direct binding bypasses the need for the 5′ cap and the scanning process. The IRES places the ribosome at or near the correct initiation site, allowing for a targeted start to protein synthesis when the cap-dependent mechanism is suppressed.
Many IRES elements require helper proteins known as IRES Trans-Acting Factors (ITAFs), and different IRESs rely on different ITAFs. These factors can act as RNA chaperones to maintain the IRES’s 3D shape or as adaptors that bridge the IRES to ribosomal components. The involvement of ITAFs adds a layer of regulation, allowing the cell to control the activity of specific IRESs.
Biological Roles of IRES Elements
IRES elements are used by viruses and by host cells during periods of stress. Viruses like poliovirus and Hepatitis C virus (HCV) carry IRES elements in their genetic material, allowing them to take over the host cell’s protein machinery for replication. These viruses often shut down the host’s cap-dependent translation, for example by cleaving the eIF4G protein, which frees up ribosomes for their own IRES-driven translation.
A cell’s own genes also contain IRES elements. During periods of cellular stress, such as hypoxia or nutrient deprivation, the cell reduces cap-dependent translation to conserve energy. However, IRES-mediated translation ensures the synthesis of proteins needed to manage the stress and promote survival.
This mechanism is also active during normal physiological processes. For example, during mitosis, overall cap-dependent translation is suppressed. The production of proteins that regulate cell division and growth continues through IRES elements in their mRNAs. This selective translation ensures these proteins are available when needed.
IRES in Biotechnology and Disease
The function of IRES elements makes them a tool in biotechnology and a subject of disease research. In molecular biology, IRES sequences are used to create bicistronic expression vectors. By placing an IRES between the coding sequences for two genes on a single mRNA, researchers can produce both proteins from one transcript. This is useful for tracking a target protein by linking its expression to a fluorescent reporter like GFP.
Because IRESs are used by viruses and are active in conditions like cancer, they are potential therapeutic targets. Many proteins that contribute to tumor growth are synthesized via IRES-dependent mechanisms, particularly in the stressful tumor microenvironment. Developing drugs to block a viral or cancer-related IRES or inhibit its interaction with ITAFs is a promising strategy for new antiviral and anticancer therapies.