A structural model of the active ribosome-bound membrane protein insertase YidC

The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.

Cells are surrounded by a plasma membrane that acts like a barrier to help to keep the cell intact. Proteins are embedded in this plasma membrane; and some of these membrane proteins act as channels that allow molecules to enter and leave the cell, while others allow the cell to communicate with its surroundings. Like all proteins, membrane proteins are chains of amino acids that are joined together by a molecular machine called a ribosome. Most membrane proteins are inserted into the membrane as they are being built. All bacteria contain a protein called YidC that inserts proteins into the plasma membrane of bacterial cells. However, the mechanism behind this activity and the parts of the YidC protein that interact with the ribosome and plasma membrane are unknown. Wickles et al. have now used data from a range of sources to predict the three-dimensional structure of the YidC protein taken from a bacterium called E. coli. The model shows how the YidC protein is threaded back-and-forth through the membrane, a total of five times. Some of the protein also extends into the inside of the bacterial cell. Wickles et al. then used a technique called cyro-electron microscopy to look at the structure of a YidC protein bound to a ribosome that is building a new protein. Fitting the more detailed model of YidC into this overall structure of the whole complex revealed how a single YidC protein might interact with the ribosome to insert a newly built protein into a membrane. Wickles et al. then used a combination of theoretical modeling and other experiments to identify the amino acids in the YidC protein that bind to the ribosome: as expected, the binding takes place where the newly formed protein chain exits the ribosome. Further experiments also identified the amino acids in the YidC protein that interact with the newly built membrane protein, thus revealing where it might leave the YidC protein and be inserted into the membrane. The next challenge will be to investigate how the YidC protein assists the folding of new membrane proteins into their own highly specific three-dimensional structure.

The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.

Cells are surrounded by a plasma membrane that acts like a barrier to help to keep the cell intact. Proteins are embedded in this plasma membrane; and some of these membrane proteins act as channels that allow molecules to enter and leave the cell, while others allow the cell to communicate with its surroundings. Like all proteins, membrane proteins are chains of amino acids that are joined together by a molecular machine called a ribosome. Most membrane proteins are inserted into the membrane as they are being built. All bacteria contain a protein called YidC that inserts proteins into the plasma membrane of bacterial cells. However, the mechanism behind this activity and the parts of the YidC protein that interact with the ribosome and plasma membrane are unknown. Wickles et al. have now used data from a range of sources to predict the three-dimensional structure of the YidC protein taken from a bacterium called E. coli. The model shows how the YidC protein is threaded back-and-forth through the membrane, a total of five times. Some of the protein also extends into the inside of the bacterial cell. Wickles et al. then used a technique called cyro-electron microscopy to look at the structure of a YidC protein bound to a ribosome that is building a new protein. Fitting the more detailed model of YidC into this overall structure of the whole complex revealed how a single YidC protein might interact with the ribosome to insert a newly built protein into a membrane. Wickles et al. then used a combination of theoretical modeling and other experiments to identify the amino acids in the YidC protein that bind to the ribosome: as expected, the binding takes place where the newly formed protein chain exits the ribosome. Further experiments also identified the amino acids in the YidC protein that interact with the newly built membrane protein, thus revealing where it might leave the YidC protein and be inserted into the membrane. The next challenge will be to investigate how the YidC protein assists the folding of new membrane proteins into their own highly specific three-dimensional structure.