Internal Ribosome Entry Sites (IRES) are genetic elements that play a unique role in protein synthesis. While most protein production begins at the start of a messenger RNA (mRNA) molecule, IRES sequences offer an alternative pathway. These RNA structures allow the cellular machinery to initiate protein synthesis from an internal position within an mRNA, bypassing typical starting signals. This ability makes IRES sequences a subject of scientific interest, particularly in understanding how cells and viruses adapt their protein production under varying conditions.
Understanding IRES Sequences
IRES sequences are regions within an mRNA molecule that enable cap-independent translation initiation. In most eukaryotic cells, protein synthesis begins when the ribosome recognizes a modified cap structure at the 5′ end of the mRNA. This cap guides the ribosome to the starting point. IRES elements, however, provide a direct entry point for the ribosome at an internal location, bypassing the 5′ cap. These elements are often found in the 5′ untranslated region (5′ UTR) of an mRNA.
Their function independent of the 5′ cap is due to their distinct secondary or tertiary structures. Their unique folding allows them to directly recruit the ribosomal machinery. This method of translation initiation is important when the standard cap-dependent pathway is hindered, such as during cellular stress or viral infections.
The Mechanism of IRES Function
IRES sequences initiate protein synthesis by directly recruiting the ribosome to an internal site on the mRNA. Normally, the small ribosomal subunit (40S) attaches to the 5′ cap and then scans along the mRNA until it finds the correct start codon. With an IRES, this scanning process is largely bypassed.
The IRES element provides signals for the 40S ribosomal subunit to bind directly to the mRNA, often near the initiation codon. This process involves interactions with various eukaryotic initiation factors (eIFs), which are proteins that usually assist in cap-dependent translation. Different IRES types vary in their specific eIF requirements. For example, some IRESs, like those found in Hepatitis C virus (HCV), can directly bind the 40S ribosomal subunit and require certain eIFs, while others, like those from picornaviruses, are recruited through eIF4G.
Beyond canonical eIFs, many IRES elements, both viral and cellular, also depend on additional proteins called IRES-trans-acting factors (ITAFs) to mediate their function. ITAFs help stabilize the three-dimensional structure of the IRES, allowing for efficient ribosome binding and proper positioning for translation. The exact roles of these ITAFs and mechanisms of some cellular IRESs remain areas of ongoing research.
Natural Occurrence of IRES Sequences
IRES sequences are found in a variety of natural contexts, playing roles in both viral replication and cellular regulation. They were first identified in 1988 in the RNA genomes of picornaviruses, such as poliovirus and encephalomyocarditis virus (EMCV). Many viruses, especially those with uncapped RNA genomes, rely on IRES elements to produce their proteins, often by hijacking the host cell’s translational machinery. This allows viruses to continue protein synthesis even when the host cell’s normal cap-dependent translation is inhibited, a strategy by which viruses ensure their survival.
IRES elements have also been identified in some cellular mRNAs. These cellular IRESs are often located in genes that encode proteins involved in stress responses, cell cycle regulation, or programmed cell death (apoptosis). Their presence allows for the continued synthesis of these proteins when overall cap-dependent translation is suppressed, providing a regulatory advantage for the cell to adapt or respond to adverse conditions. For instance, IRES-mediated translation can ensure the production of proteins needed for cell survival during periods of heat shock or nutrient deprivation.
Applications of IRES Sequences
The ability of IRES sequences to initiate translation internally has made them valuable tools in molecular biology and biotechnology. A primary application is in genetic engineering, where IRES elements are used to co-express multiple genes from a single mRNA molecule. This creates a “polycistronic” mRNA, similar to some viral genomes, allowing for the simultaneous production of several proteins from one transcriptional unit. For example, in research vectors, an IRES can be placed between two genes, ensuring both are translated even if only the first gene benefits from the 5′ cap.
This co-expression capability is useful in creating genetically modified animal models, with hundreds developed using IRES sequences. Engineered IRES variants, such as IRES2, have been developed to optimize translation efficiency. IRES sequences also hold promise in gene therapy research, especially for conditions like cancer and ischemic diseases, where therapeutic genes may need to be expressed under hypoxic (low oxygen) conditions that inhibit cap-dependent translation. Targeting IRES elements or their interacting factors (ITAFs) is also being explored for new therapeutic strategies for various diseases, including neurological and cardiovascular disorders.