Bacterial initiation factor

A bacterial initiation factor (IF) is a protein that stabilizes the initiation complex for polypeptide translation.

Translation initiation is essential to protein synthesis and regulates mRNA translation fidelity and efficiency in bacteria.^[1] The 30S ribosomal subunit, initiator tRNA, and mRNA form an initiation complex for elongation.^[2] This complex process requires three essential protein factors in bacteria – IF1, IF2, and IF3.^[3] These factors bind to the 30S subunit and promote correct initiation codon selection on the mRNA.^[4] IF1, the smallest factor at 8.2 kDa, blocks elongator tRNA binding at the A-site.^[5] IF2 is the major component that transports initiator tRNA to the P-site.^[6] IF3 checks P-site codon-anticodon pairing and rejects incorrect initiation complexes.^[7]

The orderly mechanism of initiation starts with IF3 attaching to the 30S subunit and changing its shape.^[8] IF1 joins next, followed by mRNA binding, and starts codon-P-site interaction.^[9] IF2 enters with the initiator tRNA and places it on the start codon.^[6] GTP hydrolysis by IF2 releases it and IF3, enabling 50S subunit joining.^[10] The coordinated binding and activities of IF1, IF2, and IF3 are essential for the rapid and precise translation initiation in bacteria. They facilitate start codon selection and assemble an active, protein-synthesis-ready 70S ribosome.

IF1

The IF2 initiation factor is a crucial component in the process of protein synthesis. The largest among the three indispensable translation initiation factors is IF-2, which possesses a molecular mass of 97 kDa.^[17][18] The protein has many domains, including an N-terminal domain, a GTPase domain, a linker region, C1, C2, and C-terminal domains. The GTPase domain encompasses the G1-G5 motif, which is responsible for the binding and hydrolysis of GTP.^[19] The activity of IF2 is regulated by conformational changes induced by the binding and hydrolysis of GTP.^[6] The primary function of IF-2 is to transport the initiator fMet-tRNA to the P-site of the 30S ribosomal subunit.^[20] The C2 domain of IF2 has a unique recognition and binding affinity towards the initiator tRNA. The IF-2 protein has been observed to form a ternary complex when interacting with GTP and fMet-tRNA.^[21] This complex has been found to interact with the 30S subunit.^[6] The initiation of mRNA translation involves the placement of the start codon in the P-site through the codon-anticodon base matching with the tRNA anti-codon.^[22] IF2 regulates start codon selection accuracy and inhibits elongator tRNAs' binding by selectively binding to fMet-tRNA.^[23] Additionally, it relocates the initiator tRNA on the 30S subunit to enhance the optimum contact with the P-site.^[24] Furthermore, IF2 exhibits RNA chaperone activity, which enables it to rectify misfolded RNA structures. In general, the IF2 protein plays a crucial role in coordinating many steps of translation initiation, including the binding of mRNA and fMet-tRNA to the start codon, the joining of sub-units, and the activation of GTPase.

IF3

Initiation factor IF3 is a small protein of 21 kDa containing two compact α/β domains (IF3C and IF3N) connected by a flexible lysine-rich linker.