Bacterial Transmembrane Proteins Research Articles

Computational Study of Transmembrane Helix-Helix Interactions in Model Peptides Derived from the DesK Minimal Sensor

DesK is a bacterial transmembrane protein that acts as a molecular switch to regulate membrane fluidity as a function of temperature change. The full function of DesK has been experimentally modeled by a chimeric construct, denominated minimal sensor (MS), consisting of a single transmembrane (TM) helix. Multiple mutants based on the TM part of DesK-MS have been reported, suggesting that DesK is sensitive to changes in membrane thickness as a result of changes in temperature. The current view of DesK-MS signaling mechanism points towards formation of a dimer capable of switching its conformation depending on the temperature.In this study we investigate the molecular details of the functioning of the DesK-MS using experimentally developed model peptides of the TM part only, both the wild type and some of its mutants. We employ a method recently developed in our group for exploring the energy landscape of helix-helix interactions in the membrane environment, which allows high throughput screening of trans-membrane helix dimers. In order to gain more insight into the interactions between the dimers and their lipid environment, a multiscale approach is used. The results presented here are compared to the available experimental data and provide basis for further exploration of the molecular basis of the switch mechanism in DesK-MS.

Bacterial Transmembrane Proteins that Lack N-Terminal Signal Sequences

Tail-anchored membrane proteins (TAMPs), a class of proteins characterized by their lack of N-terminal signal sequence and Sec-independent membrane targeting, play critical roles in apoptosis, vesicle trafficking and other vital processes in eukaryotic organisms. Until recently, this class of membrane proteins has been unknown in bacteria. Here we present the results of bioinformatic analysis revealing proteins that are superficially similar to eukaryotic TAMPs in the bacterium Streptomyces coelicolor. We demonstrate that at least four of these proteins are bona fide membrane-spanning proteins capable of targeting to the membrane in the absence of their N-terminus and the C-terminal membrane-spanning domain is sufficient for membrane targeting. Several of these proteins, including a serine/threonine kinase and the SecE component of the Sec translocon, are widely conserved in bacteria.

Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella

Homologues of the protein constituents of the Klebsiella pneumoniae (Klebsiella oxytoca) type II secreton (T2S), the Pseudomonas aeruginosa type IV pilus/fimbrium biogenesis machinery (T4P) and the Methanococcus voltae flagellum biogenesis machinery (Fla) have been identified. Known constituents of these systems include (1). a major prepilin (preflagellin), (2). several minor prepilins (preflagellins), (3). a prepilin (preflagellin) peptidase/methylase, (4). an ATPase, (5). a multispanning transmembrane (TM) protein, (6). an outer-membrane secretin (lacking in Fla) and (7). several functionally uncharacterized envelope proteins. Sequence and phylogenetic analyses led to the conclusion that, although many of the protein constituents are probably homologous, extensive sequence divergence during evolution clouds this homology so that a common ancestry can be established for all three types of systems for only two constituents, the ATPase and the TM protein. Sequence divergence of the individual T2S constituents has occurred at characteristic rates, apparently without shuffling of constituents between systems. The same is probably also true for the T4P and Fla systems. The family of ATPases is much larger than the family of TM proteins, and many ATPase homologues function in capacities unrelated to those considered here. Many phylogenetic clusters of the ATPases probably exhibit uniform function. Some of these have a corresponding TM protein homologue although others probably function without one. It is further shown that proteins that compose the different phylogenetic clusters in both the ATPase and the TM protein families exhibit unique structural characteristics that are of probable functional significance. The TM proteins are shown to have arisen by at least two dissimilar intragenic duplication events, one in the bacterial kingdom and one in the archaeal kingdom. The archaeal TM proteins are twice as large as the bacterial TM proteins, suggesting an oligomeric structure for the latter.