Biological functions of the ribosomal exit tunnel

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SecA is an ATPase that drives protein export across the bacterial cytoplasmic membrane, through the SecYEG translocon. In E. coli the gene secA is preceded by an open reading frame called gene X or secM (secretion monitor), which comprises an operon with secA. Our characterization of the gene X product revealed that it contains an "arrest sequence" that interacts with the exit tunnel of the ribosome to halt translation elongation. We showed that the elongation arrest is essential for the basal level expression of SecA as well as for its up-regulation under the conditions (such as low temperture) of impaired protein secretion. Moreover, our results suggest that SecM falicilitates the functionalization of newly synthesized SecA molecules, presumably by localizing its biosynthesis to the vicinity of the membrane/ translocon, a function we refer to "cis-chaperone". Thus, SecM functions exclusively in its nascent ribosome-tethered state and contains a sequence that cannot be elongated in ribosomal translation unless the N-terminal region outside the ribosome interacts with the Sec machinery. We investigated the mechanism of elongation arrest using in vitro translation system with purified translation components and revealed that the SecM peculiarity includes the fact that its Pro166 codon specifies ribosomal A-site located prolyl-tRNA that functions as an effector of the elongation arrest without being incorporated into the polypeptide chain.