The Cytoplasmic Domains of Streptococcus mutans Membrane Protein Insertases YidC1 and YidC2 Confer Unique Structural and Functional Attributes to Each Paralog

Integral and membrane-anchored proteins are pivotal to survival and virulence of the dental pathogen, Streptococcus mutans. The bacterial chaperone/insertase, YidC, contributes to membrane protein translocation. Unlike Escherichia coli, most Gram-positive bacteria contain two YidC paralogs. Herein, we evaluated structural features that functionally delineate S. mutans YidC1 and YidC2. Bacterial YidCs contain five transmembrane domains (TMD), two cytoplasmic loops, and a cytoplasmic tail. Because S. mutans YidC1 (SmYidC1) and YidC2 (SmYidC2) cytoplasmic domains (CD) are less well conserved than are TMD, we engineered ectopic expression of the 14 possible YidC1-YidC2 CD domain swap combinations. Growth and stress tolerance of each was compared to control strains ectopically expressing unmodified yidC1 or yidC2. Acid and osmotic stress sensitivity are associated with yidC2 deletion. Sensitivity to excess zinc was further identified as a ΔyidC1 phenotype. Overall, YidC1 tolerated CD substitutions better than YidC2. Preferences toward particular CD combinations suggested potential intramolecular interactions. In silico analysis predicted salt-bridges between C1 and C2 loops of YidC1, and C1 loop and C-terminal tail of YidC2, respectively. Mutation of contributing residues recapitulated ΔyidC1- and ΔyidC2-associated phenotypes. Taken together, this work revealed the importance of cytoplasmic domains in distinct functional attributes of YidC1 and YidC2, and identified key residues involved in interdomain interactions.

Role of the Cytosolic Loop C2 and the C Terminus of YidC in Ribosome Binding and Insertion Activity

Members of the YidC/Oxa1/Alb3 protein family mediate membrane protein insertion, and this process is initiated by the assembly of YidC·ribosome nascent chain complexes at the inner leaflet of the lipid bilayer. The positively charged C terminus of Escherichia coli YidC plays a significant role in ribosome binding but is not the sole determinant because deletion does not completely abrogate ribosome binding. The positively charged cytosolic loops C1 and C2 of YidC may provide additional docking sites. We performed systematic sequential deletions within these cytosolic domains and studied their effect on the YidC insertase activity and interaction with translation-stalled (programmed) ribosome. Deletions within loop C1 strongly affected the activity of YidC in vivo but did not influence ribosome binding or substrate insertion, whereas loop C2 appeared to be involved in ribosome binding. Combining the latter deletion with the removal of the C terminus of YidC abolished YidC-mediated insertion. We propose that these two regions play an crucial role in the formation and stabilization of an active YidC·ribosome nascent chain complex, allowing for co-translational membrane insertion, whereas loop C1 may be involved in the downstream chaperone activity of YidC or in other protein-protein interactions.

Compaction of a prokaryotic signal-anchor transmembrane domain begins within the ribosome tunnel and is stabilized by SRP during targeting

Cotranslational targeting of membrane proteins is mediated by the universally conserved signal recognition particle (SRP). In eukaryotes, SRP attenuates translation during targeting; however, in prokaryotes, a simplified SRP is believed to carry out targeting during continuing translation. Here, we show a detailed stepwise analysis of the targeting of subunit c of the F(0) component of the bacterial ATP synthase (F(0)c) to the inner membrane. We show that the first transmembrane (TM) signal-anchor domain of F(0)c forms a compacted structure within the distal portion of the ribosome tunnel. This structure is formed just prior to the interaction with SRP. In the absence of SRP this structure is lost as the TM domain exits the tunnel; however in the presence of SRP it is stabilized. Our results suggest differences in early protein folding of substrates for prokaryotic SRP-dependent membrane protein targeting pathways, from that of eukaryotic SRP targeting. These results imply that early TM domain recognition by targeting factors acts to ensure that the efficiency of membrane targeting is maintained.

Biogenesis of bacterial inner-membrane proteins

All cells must traffic proteins into and across their membranes. In bacteria, several pathways have evolved to enable protein transfer across the inner membrane, the periplasm, and the outer membrane. The major route of protein translocation in and across the cytoplasmic membrane is the general secretion pathway (Sec-pathway). The biogenesis of membrane proteins not only requires protein translocation but also coordinated targeting to the membrane beforehand and folding and assembly into their protein complexes afterwards to function properly in the cell. All these processes are responsible for the biogenesis of membrane proteins that mediate essential functions of the cell such as selective transport, energy conversion, cell division, extracellular signal sensing, and motility. This review will highlight the most recent developments on the structure and function of bacterial membrane proteins, focusing on the journey that integral membrane proteins take to find their final destination in the inner membrane.

Mechanisms of YidC-mediated insertion and assembly of multimeric membrane protein complexes

The YidC protein fulfills a dual and essential role in the assembly of inner membrane proteins in Escherichia coli. Besides interacting with transmembrane segments of newly synthesized membrane proteins that insert into the membrane via the SecYEG complex, YidC also functions as an independent membrane protein insertase and assists in membrane protein folding. Here, we discuss the mechanisms of YidC substrate recognition and membrane insertion with emphasis on its role in the assembly of multimeric membrane protein complexes such as the F1F0-ATP synthase.