Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A unified model for BAM function that takes into account type Vc secretion and species differences in BAM composition.

ABSTRACT: Transmembrane proteins in the outer membrane of Gram-negative bacteria are almost exclusively ?-barrels. They are inserted into the outer membrane by a conserved and essential protein complex called the BAM (for ?-barrel assembly machinery). In this commentary, we summarize current research into the mechanism of this protein complex and how it relates to type V secretion. Type V secretion systems are autotransporters that all contain a ?-barrel transmembrane domain inserted by BAM. In type Vc systems, this domain is a homotrimer. We argue that none of the current models are sufficient to explain BAM function particularly regarding type Vc secretion. We also find that current models based on the well-studied model system Escherichia coli mostly ignore the pronounced differences in BAM composition between different bacterial species. We propose a more holistic view on how all OMPs, including autotransporters, are incorporated into the lipid bilayer.

SUBMITTER: Leo JC

PROVIDER: S-EPMC6604945 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A unified model for BAM function that takes into account type Vc secretion and species differences in BAM composition.

Leo Jack C JC Linke Dirk D

AIMS microbiology 20180622 3

Transmembrane proteins in the outer membrane of Gram-negative bacteria are almost exclusively β-barrels. They are inserted into the outer membrane by a conserved and essential protein complex called the BAM (for β-barrel assembly machinery). In this commentary, we summarize current research into the mechanism of this protein complex and how it relates to type V secretion. Type V secretion systems are autotransporters that all contain a β-barrel transmembrane domain inserted by BAM. In type Vc sy ...[more]

PMID: 31294227

Similar Datasets

pH-regulated mechanisms account for pigment-type differences in epidermal barrier function.

Project description:To determine whether pigment type determines differences in epidermal function, we studied stratum corneum (SC) pH, permeability barrier homeostasis, and SC integrity in three geographically disparate populations with pigment type I-II versus IV-V skin (Fitzpatrick I-VI scale). Type IV-V subjects showed: (i) lower surface pH (approximately 0.5 U); (ii) enhanced SC integrity (transepidermal water loss change with sequential tape strippings); and (iii) more rapid barrier recovery than type I-II subjects. Enhanced barrier function could be ascribed to increased epidermal lipid content, increased lamellar body production, and reduced acidity, leading to enhanced lipid processing. Compromised SC integrity in type I-II subjects could be ascribed to increased serine protease activity, resulting in accelerated desmoglein-1 (DSG-1)/corneodesmosome degradation. In contrast, DSG-1-positive CDs persisted in type IV-V subjects, but due to enhanced cathepsin-D activity, SC thickness did not increase. Adjustment of pH of type I-II SC to type IV-V levels improved epidermal function. Finally, dendrites from type IV-V melanocytes were more acidic than those from type I-II subjects, and they transfer more melanosomes to the SC, suggesting that melanosome secretion could contribute to the more acidic pH of type IV-V skin. These studies show marked pigment-type differences in epidermal structure and function that are pH driven.

| S-EPMC2695842 | biostudies-literature

Allelic Differences Account for Gene Expression Differences Among Population.

Project description:Expression level of genes in lymphoblasts from individuals in three HapMap populations (CEU, CHB, JPT) were compared. More than 1,000 genes were found to be significantly different (Pc<0.05) in mean expression level between the CEU and CHB+JPT samples. Keywords: Comparison of Gene Expression Profiles from Lymphoblastoid cells

2007-01-07 | GSE5859 | GEO

COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.

Project description:Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary structure are thermodynamic methods. These aim to predict the most stable RNA structure. There exists by now ample experimental and theoretical evidence that the process of structure formation matters and that sequences in vivo fold while they are being transcribed. None of the thermodynamic methods, however, consider the process of structure formation. Here, we present a conceptually new method for predicting RNA secondary structure, called CoFold, that takes effects of co-transcriptional folding explicitly into account. Our method significantly improves the state-of-art in terms of prediction accuracy, especially for long sequences of >1000 nt in length.

| S-EPMC3643587 | biostudies-literature

Randomization in survival studies: An evaluation method that takes into account selection and chronological bias.

Project description:The random allocation of patients to treatments is a crucial step in the design and conduct of a randomized controlled trial. For this purpose, a variety of randomization procedures is available. In the case of imperfect blinding, the extent to which a randomization procedure forces balanced group sizes throughout the allocation process affects the predictability of allocations. As a result, some randomization procedures perform superior with respect to selection bias, whereas others are less susceptible to chronological bias. The choice of a suitable randomization procedure therefore depends on the expected risk for selection and chronological bias within the particular study in question. To enable a sound comparison of different randomization procedures, we introduce a model for the combined effect of selection and chronological bias in randomized studies with a survival outcome. We present an evaluation method to quantify the influence of bias on the test decision of the log-rank test in a randomized parallel group trial with a survival outcome. The effect of selection and chronological bias and the dependence on the study setting are illustrated in a sensitivity analysis. We conclude with a case study to showcase the application of our model for comparing different randomization procedures in consideration of the expected type I error probability.

| S-EPMC6546249 | biostudies-literature

Overproducing the BAM complex improves secretion of difficult-to-secrete recombinant autotransporter chimeras.

Project description:Monomeric autotransporters have been used extensively to transport recombinant proteins or protein domains to the cell surface of Gram-negative bacteria amongst others for antigen display. Genetic fusion of such antigens into autotransporters has yielded chimeras that can be used for vaccination purposes. However, not every fusion construct is transported efficiently across the cell envelope. Problems occur in particular when the fused antigen attains a relatively complex structure in the periplasm, prior to its translocation across the outer membrane. The latter step requires the interaction with periplasmic chaperones and the BAM (β-barrel assembly machinery) complex in the outer membrane. This complex catalyzes insertion and folding of β-barrel outer membrane proteins, including the β-barrel domain of autotransporters. Here, we investigated whether the availability of periplasmic chaperones or the BAM complex is a limiting factor for the surface localization of difficult-to-secrete chimeric autotransporter constructs. Indeed, we found that overproduction of in particular the BAM complex, increases surface display of difficult-to-secrete chimeras. Importantly, this beneficial effect appeared to be generic not only for a number of monomeric autotransporter fusions but also for fusions to trimeric autotransporters. Therefore, overproduction of BAM might be an attractive strategy to improve the production of recombinant autotransporter constructs.

| S-EPMC8419823 | biostudies-literature

A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel's second law.

Project description:Comparative studies in evolutionary genetics rely critically on evaluation of the total amount of genetic shuffling that occurs during gamete production. Such studies have been hampered by the absence of a direct measure of this quantity. Existing measures consider crossing-over by simply counting the average number of crossovers per meiosis. This is qualitatively inadequate, because the positions of crossovers along a chromosome are also critical: a crossover toward the middle of a chromosome causes more shuffling than a crossover toward the tip. Moreover, traditional measures fail to consider shuffling from independent assortment of homologous chromosomes (Mendel's second law). Here, we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations. We define the parameter [Formula: see text] as the probability that the alleles at two randomly chosen loci are shuffled during gamete production. This measure can be decomposed into separate contributions from crossover number and position and from independent assortment. Intrinsic implications of this metric include the fact that [Formula: see text] is larger when crossovers are more evenly spaced, which suggests a selective advantage of crossover interference. Utilization of [Formula: see text] is enabled by powerful emergent methods for determining crossover positions either cytologically or by DNA sequencing. Application of our analysis to such data from human male and female reveals that (i) [Formula: see text] in humans is close to its maximum possible value of 1/2 and that (ii) this high level of shuffling is due almost entirely to independent assortment, the contribution of which is ∼30 times greater than that of crossovers.

| S-EPMC6358705 | biostudies-literature

Myosin vc interacts with Rab32 and Rab38 proteins and works in the biogenesis and secretion of melanosomes.

Project description:Class V myosins are actin-based motors with conserved functions in vesicle and organelle trafficking. Herein we report the discovery of a function for Myosin Vc in melanosome biogenesis as an effector of melanosome-associated Rab GTPases. We isolated Myosin Vc in a yeast two-hybrid screening for proteins that interact with Rab38, a Rab protein involved in the biogenesis of melanosomes and other lysosome-related organelles. Rab38 and its close homolog Rab32 bind to Myosin Vc but not to Myosin Va or Myosin Vb. Binding depends on residues in the switch II region of Rab32 and Rab38 and regions of the Myosin Vc coiled-coil tail domain. Myosin Vc also interacts with Rab7a and Rab8a but not with Rab11, Rab17, and Rab27. Although Myosin Vc is not particularly abundant on pigmented melanosomes, its knockdown in MNT-1 melanocytes caused defects in the trafficking of integral membrane proteins to melanosomes with substantially increased surface expression of Tyrp1, nearly complete loss of Tyrp2, and significant Vamp7 mislocalization. Knockdown of Myosin Vc in MNT-1 cells more than doubled the abundance of pigmented melanosomes but did not change the number of unpigmented melanosomes. Together the data demonstrate a novel role for Myosin Vc in melanosome biogenesis and secretion.

| S-EPMC4246105 | biostudies-literature

Corticosteroid-binding globulin: structure-function implications from species differences.

Project description:Corticosteroid-binding globulin (CBG) transports glucocorticoids and progesterone in the blood and thereby modulates the tissue availability of these hormones. As a member of the serine protease inhibitor (SERPIN) family, CBG displays a reactive center loop (RCL) that is targeted by proteinases. Cleavage of the RCL is thought to trigger a SERPIN-typical stressed-to-relaxed (S-to-R) transition that leads to marked structural rearrangements and a reduced steroid-binding affinity. To characterize structure-function relationships in CBG we studied various conformational states of E. coli-produced rat and human CBG. In the 2.5 Å crystal structure of human CBG in complex with progesterone, the RCL is cleaved at a novel site that differs from the known human neutrophil elastase recognition site. Although the cleaved RCL segment is five residues longer than anticipated, it becomes an integral part of β-sheet A as a result of the S-to-R transition. The atomic interactions observed between progesterone and CBG explain the lower affinity of progesterone in comparison to corticosteroids. Surprisingly, CD measurements in combination with thermal unfolding experiments show that rat CBG fails to undergo an S-to-R transition upon proteolytic cleavage of the RCL hinting that the S-to-R transition observed in human CBG is not a prerequisite for CBG function in rat. This observation cautions against drawing general conclusions about molecular mechanisms by comparing and merging structural data from different species.

| S-EPMC3530532 | biostudies-literature

Glycosylation of procathepsin L does not account for species molecular-mass differences and is not required for proteolytic activity.

Project description:Cathepsin L is a major lysosomal cysteine proteinase in mouse and human cells. Despite similar predicted molecular masses, procathepsin L in these two species migrates on SDS/polyacrylamide gels with apparent molecular masses of 39 kDa and 42 kDa respectively. To determine if glycosylation differences account for this discrepancy, and to ascertain whether glycosylation is essential for enzymic activity, mouse and human procathepsins L were expressed at high concentrations in mouse NIH 3T3 cells or in human A431 cells after DNA-mediated transfection of cloned DNAs for these enzymes. In pulse-chase studies, human procathepsin L transfectants synthesized and secreted large amounts of enzymically active 42 kDa proenzyme and processed it into 34 kDa and 26 kDa intracellular peptides, a pattern of secretion and processing similar to that seen with endogenous or transfected mouse procathepsin L. Both translation of cloned procathepsin L cDNAs in vitro and Endoglycosidase H treatment of 39 kDa mouse and 42 kDa human procathepsin L resulted in non-glycosylated proteins 2 kDa lower in molecular mass than the untreated proteins for both species. This suggests that glycosylation differences are not responsible for the molecular-mass disparity between the two species. Moreover, Endoglycosidase H-treated mouse enzyme retained full proteolytic activity, indicating that glycosylation of cathepsin L is not essential for enzymic function.

| S-EPMC1133362 | biostudies-other

Coral species composition drives key ecosystem function on coral reefs.

Project description:Rapid and unprecedented ecological change threatens the functioning and stability of ecosystems. On coral reefs, global climate change and local stressors are reducing and reorganizing habitat-forming corals and associated species, with largely unknown implications for critical ecosystem functions such as herbivory. Herbivory mediates coral-algal competition, thereby facilitating ecosystem recovery following disturbance such as coral bleaching events or large storms. However, relationships between coral species composition, the distribution of herbivorous fishes and the delivery of their functional impact are not well understood. Here, we investigate how herbivorous fish assemblages and delivery of two distinct herbivory processes, grazing and browsing, differ among three taxonomically distinct, replicated coral habitats. While grazing on algal turf assemblages was insensitive to different coral configurations, browsing on the macroalga Laurencia cf. obtusa varied considerably among habitats, suggesting that different mechanisms may shape these processes. Variation in browsing among habitats was best predicted by the composition and structural complexity of benthic assemblages (in particular the cover and composition of corals, but not macroalgal cover), and was poorly reflected by visual estimates of browser biomass. Surprisingly, the lowest browsing rates were recorded in the most structurally complex habitat, with the greatest cover of coral (branching Porites habitat). While the mechanism for the variation in browsing is not clear, it may be related to scale-dependent effects of habitat structure on visual occlusion inhibiting foraging activity by browsing fishes, or the relative availability of alternate dietary resources. Our results suggest that maintained functionality may vary among distinct and emerging coral reef configurations due to ecological interactions between reef fishes and their environment determining habitat selection.

| S-EPMC7062023 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data