Residue-by-residue analysis of cotranslational membrane protein integration in vivo

Abstract

We follow the cotranslational biosynthesis of three multi-spanning E. coli inner membrane proteins in vivo using high-resolution Force Profile Analysis. The force profiles show that the nascent chain is subjected to rapidly varying pulling forces during translation, and reveal unexpected complexities in the membrane integration process. We find that an N-terminal cytoplasmic domain can fold in the ribosome exit tunnel before membrane integration starts, that charged residues and membrane-interacting segments such as re-entrant loops and surface helices flanking a transmembrane helix (TMH) can advance or delay membrane integration, and that point mutations in an upstream TMH can affect the pulling forces generated by downstream TMHs in a highly position-dependent manner, suggestive of residue-specific interactions between TMHs during the integration process. Our results support the 'sliding' model of translocon-mediated membrane protein integration, in which hydrophobic segments are continually exposed to the lipid bilayer during their passage through the SecYEG translocon.

Methodologies for Measuring Protein Trafficking across Cellular Membranes

“…To understand how the biochemistry of cotranslational protein translocation quantitatively impacts the force exerted on the nascent substrate, Hessa and colleagues have recently measured the protein translocation force in mammalian Sec61 translocon. [49] Their approach takes advantage of the ribosome arrest peptide (RAP) [50][51][52] of X-box binding protein 1 (Xbp1).…”

Folding and Insertion of Transmembrane Helices at the ER

“…Recent evidence has implicated the EMC in helping to establish the topology of the first TM of many GPCRs and likely other proteins [ 12 , 72 ]. The translocon’s lateral gate allows direct sampling of the membrane environment by the TM [ 73 ], possibly from the moment of its encounter with the translocon [ 39 , 74 ]. The code for insertion, i.e., what sequences partition to the membrane vs. remain in the channel, has been determined in exquisite detail with extensive, elegant experiments from von Heijne, White, and colleagues in the mid-2000s [ 31 , 32 ].…”

Upstream charged and hydrophobic residues impact the timing of membrane insertion of transmembrane helices

“…While the energetics of membrane insertion of transmembrane helices (TMHs) has been extensively studied both in vitro and in vivo [3–6], it is only recently that methodologies have been developed that make it possible to follow step-by-step the membrane insertion of individual TMHs as they come out of the ribosome exit tunnel. Two methods in particular can provide this kind of information: in vitro real-time FRET analysis of cotranslational membrane insertion [7] and in vivo Force Profile Analysis (FPA) where a translational arrest peptide (AP) engineered into the polypeptide chain is used to detect the force generated on the nascent chain during membrane insertion [8,9].…”

“…In a recent study, we applied FPA to three E. coli inner membrane proteins: EmrE, GlpG, and BtuC [9]. For all three proteins (a total of 20 TMHs), we found that, on average, a TMH starts to generate force on the nascent chain when its N-terminal end is ~45 residues away from the polypeptide transferase center (PTC) in the large ribosome subunit.…”

“…Here, we focus on two such unexpected features in the FP recorded for the 10-TMH BtuC protein [9]: (i) TMH2 starts to generate force only when its N-terminal end is ~55 rather than the expected ~45 residues away from the PTC, and (ii) two narrow peaks appear in the force profile flanking the location where a single peak generated by TMH6 was expected. In particular, we ask whether these effects are peculiar to BtuC, or whether they are also seen when the segments that flank BtuC TMH2 and TMH6 are fused to a model TMH composed of Leu and Ala residues.…”