The nascent polypeptide exit site of the ribosome is a crowded environment where multiple ribosome-associated protein biogenesis factors (RPBs) compete for the nascent polypeptide to influence their localization, folding, or quality control. Here we address how N-terminal methionine excision (NME), a ubiquitous process crucial for the maturation of over 50% of the bacterial proteome, occurs in a timely and selective manner in this crowded environment. In bacteria, NME is mediated by 2 essential enzymes, peptide deformylase (PDF) and methionine aminopeptidase (MAP). We show that the reaction of MAP on ribosome-bound nascent chains approaches diffusion-limited rates, allowing immediate methionine excision of optimal substrates after deformylation. Specificity is achieved by kinetic competition of NME with translation elongation and by regulation from other RPBs, which selectively narrow the processing time window for suboptimal substrates. A mathematical model derived from the data accurately predicts cotranslational NME efficiency in the cytosol. Our results demonstrate how a fundamental enzymatic activity is reshaped by its associated macromolecular environment to optimize both efficiency and selectivity, and provides a platform to study other cotranslational protein biogenesis pathways.

Proteins are thought to be delivered to the bacterial plasma membrane cotranslationally by signal recognition particle or posttranslationally by SecA. Wang et al. identify a new membrane protein–targeting pathway in bacteria in which SecA cotranslationally recognizes and targets the inner membrane protein RodZ, which harbors an internal transmembrane domain.

Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plasma membrane. The molecular mechanism of this pathway remains unclear. Here we use biochemical and cryoelectron microscopy analyses to show that the N-terminal amphipathic helix of SecA and the ribosomal protein uL23 form a composite binding site for the transmembrane domain (TMD) on the nascent protein. This binding mode further enables recognition of charged residues flanking the nascent TMD and thus explains the specificity of SecA recognition. Finally, we show that membraneembedded SecYEG promotes handover of the translating ribosome from SecA to the translocase via a concerted mechanism. Our work provides a molecular description of the SecA-mediated cotranslational targeting pathway and demonstrates an unprecedented role of the ribosome in shielding nascent TMDs. Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

Electron microscopy is currently the most powerful method to discern the mechanisms of solid-state transformation and dissolution-reprecipitation for the studies of biomineralization. In this work, we show that solid-state NMR spectroscopy can serve as a useful complementary technique to characterize the crystallization pathway of a mineral phase. On the basis of the so-called NMR spin-diffusion method, direct evidence is given to support that the formation of the apatite phase within liposomes occurs via the solid-state transformation of the disordered phase. In this thermodynamically downhill process, the final step is the depletion of the structural water in the disordered phase, whose structural order of the phosphorus species is comparable to that of apatite.

One of the hallmarks of Alzheimers disease is the deposition of amyloid plaques, which consist of β-amyloid (Aβ) peptides in fibrillar states. Nonfibrillar Aβ aggregates have been considered as an important intermediate in the pathway of fibrillization, but little is known about the formation mechanism. The on-pathway β-sheet intermediates of Aβ40 peptides can be trapped by incubating the peptides in liposomes formed by zwitterionic lipids. The aggregates of Aβ40 peptides have been prepared at a peptide concentration of less than 10 μm. Solid-state NMR spectroscopy data show that the backbone conformation of the aggregates is almost identical to that of the fibrils formed in free solution. In contrast to anionic lipids, zwitterionic lipids, which are typical of neuronal soma, did not induce any significant conformational difference in Aβ40 fibrils. This liposome-Aβ system may serve as a useful model to study the fibril formation mechanism.