Protein uptake into E. coll during Bdellovibrio infection A process of reverse secretion?

AbstractBdellovibrio bacteriovorus is a small bacterial parasite that infects other Gram-negative bacteria, resides in the periplasm of the host cell, and utilizes host macromolecules as a source of nutrients. Evidence is summarized suggesting that B. bacteriovorus secretes proteases and nucleases synthesized in its own cytoplasm that are targeted to the cytoplasm of the host cell. Possible mechanisms for this trans-trimembrane protein transport process are discussed

Functional Promiscuity of Homologues of the Bacterial ArsA ATPases

The ArsA ATPase of E. coli plays an essential role in arsenic detoxification. Published evidence implicates ArsA in the energization of As(III) efflux via the formation of an oxyanion-translocating complex with ArsB. In addition, eukaryotic ArsA homologues have several recognized functions unrelated to arsenic resistance. By aligning ArsA homologues, constructing phylogenetic trees, examining ArsA encoding operons, and estimating the probable coevolution of these homologues with putative transporters and auxiliary proteins unrelated to ArsB, we provide evidence for new functions for ArsA homologues. They may play roles in carbon starvation, gas vesicle biogenesis, and arsenic resistance. The results lead to the proposal that ArsA homologues energize four distinct and nonhomologous transporters, ArsB, ArsP, CstA, and Acr3

Evolution of the Oligopeptide Transporter Family

The oligopeptide transporter (OPT) family of peptide and iron-siderophore transporters includes members from both prokaryotes and eukaryotes but with restricted distribution in the latter domain. Eukaryotic members were found only in fungi and plants with a single slime mold homologue clustering with the fungal proteins. All functionally characterized eukaryotic peptide transporters segregate from the known iron-siderophore transporters on a phylogenetic tree. Prokaryotic members are widespread, deriving from many different phyla. Although they belong only to the iron-siderophore subdivision, genome context analyses suggest that many of them are peptide transporters. OPT family proteins have 16 or occasionally 17 transmembrane-spanning α-helical segments (TMSs). We provide statistical evidence that the 16-TMS topology arose via three sequential duplication events followed by a gene-fusion event for proteins with a seventeenth TMS. The proposed pathway is as follows: 2 TMSs → 4 TMSs → 8 TMSs → 16 TMSs → 17 TMSs. The seventeenth C-terminal TMS, which probably arose just once, is found in just one phylogenetic group of these homologues. Analyses for orthology revealed that a few phylogenetic clusters consist exclusively of orthologues but most have undergone intermixing, suggestive of horizontal transfer. It appears that in this family horizontal gene transfer was frequent among prokaryotes, rare among eukaryotes and largely absent between prokaryotes and eukaryotes as well as between plants and fungi. These observations provide guides for future structural and functional analyses of OPT family members

Transcriptional Regulation of the rsbV Promoter Controlling Stress Responses to Ethanol, Carbon Limitation, and Phosphorous Limitation in Bacillus subtilis

The σB-dependent promoter in front of the rsbV gene of Bacillus subtilis is induced ∼5-fold in response to (1) the addition of 4% ethanol, (2) carbon starvation, and (3) phosphorous starvation. Binding sites for the global carbon and nitrogen regulators, CcpA and TnrA, were mutated, and the consequences of their loss and that of CcpA or TnrA were studied using rsbV-lacZ fusions. These responses proved to be dependent on CcpA, TnrA, and their putative binding sites upstream of the promoter. Induction in response to glucose limitation was largely abolished by loss of CcpA or the upstream region, while induction in response to phosphorous limitation was largely abolished only by the upstream mutations. The results suggest that CcpA directly influences the carbon starvation response and that both proteins exert indirect effects on all three stress responses. The integrity of the DNA sequence is important for all three responses

Bacterial Adaptor Membrane Fusion Proteins and the Structurally Dissimilar Outer Membrane Auxiliary Proteins Have Exchanged Central Domains in α-Proteobacteria

Transport systems frequently include auxiliary proteins that perform subfunctions within the transporter protein complex. Two such proteins found in Gram-negative bacteria are the Membrane Fusion Proteins (MFPs) and the Outer Membrane Auxiliary (OMA) proteins. We here demonstrate that OMAs present in α-proteobacteria (but not in other bacterial types) contain a long α-helical region that is homologous to corresponding regions in the MFPs. The results suggest that during their evolution, OMAs, specifically from α-proteobacteria, exchanged their own α-helical domain for one derived from an MFP. The structural and functional implications of these findings are discussed

TCDB: the Transporter Classification Database for membrane transport protein analyses and information

The Transporter Classification Database (TCDB) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. TCDB is a curated repository for factual information compiled from >10 000 references, encompassing ∼3000 representative transporters and putative transporters, classified into >400 families. The transporter classification (TC) system is an International Union of Biochemistry and Molecular Biology approved system of nomenclature for transport protein classification. TCDB is freely accessible at . The web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or TC number and full-text searching. The functional ontology that underlies the database structure facilitates powerful query searches that yield valuable data in a quick and easy way. The TCDB website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins. TCDB not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool

Instability and topological robustness of Weyl semimetals against Coulomb interaction

There is a close connection between various new phenomena in Weyl semimetals and the existence of linear band crossings in the single particle description. We show, by a full self-consistent mean-field calculation, how this picture is modified in the presence of long-range Coulomb interactions. The chiral symmetry breaking occurs at strong enough interactions and the internode interband excitonic pairing channel is found to be significant, which determines the gap-opened band profile varying with interaction strength. Remarkably, in the resultant interacting phase, finite band Chern number jumps in the three-dimensional momentum space are retained, indicating the robustness of the topologically nontrivial features.Comment: 8 pages, 4 figures, accepted by Phys. Rev.

Homologues of archaeal rhodopsins in plants, animals and fungi: structural and functional predications for a putative fungal chaperone protein

AbstractThe microbial rhodopsins (MR) are homologous to putative chaperone and retinal-binding proteins of fungi. These proteins comprise a coherent family that we have termed the MR family. We have used modeling techniques to predict the structure of one of the putative yeast chaperone proteins, YRO2, based on homology with bacteriorhodopsins (BR). Availability of the structure allowed depiction of conserved residues that are likely to be of functional significance. The results lead us to predict an extracellular protein folding function and a transmembrane proton transport pathway. We suggest that protein folding is energized by a novel mechanism involving the proton motive force. We further show that MR family proteins are distantly related to a family of fungal, animal and plant proteins that include the human lysosomal cystine transporter (LCT) of man (cystinosin), mutations in which cause cystinosis. Sequence and phylogenetic analyses of both the MR family and the LCT family are reported. Proteins in both families are of the same approximate size, exhibit seven putative transmembrane α-helical spanners (TMSs) and show limited sequence similarity. We show that the LCT family arose by an internal gene duplication event and that TMSs 1–3 are homologous to TMSs 5–7. Although the same could not be demonstrated statistically for MR family members, homology with the LCT family suggests (but does not prove) a common evolutionary pathway. Thus, TMSs 1–3 and 5–7 in both LCT and MR family members may share a common origin, accounting for their shared structural features