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This is the Wikipedia entry entitled "Bacterial outer membrane". More...
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Bacterial outer membrane Edit Wikipedia article
The bacterial outer membrane is found in gram-negative bacteria. Its composition is distinct from that of the inner cytoplasmic cell membrane - among other things, the outer leaflet of the outer membrane of many gram-negative bacteria includes a complex lipopolysaccharide whose lipid portion acts as an endotoxin - and in some bacteria such as E. coli it is linked to the cell's peptidoglycan by Braun's lipoprotein.
If lipid A, part of the LPS, enters the circulatory system it causes a toxic reaction by activating TLR 4. Lipid A is very pathogenic and not immunogenic. However, the polysaccharide component is very immunogenic, but not pathogenic, causing an aggressive response by the immune system. The sufferer will have a high temperature and respiration rate and a low blood pressure. This may lead to endotoxic shock, which may be fatal. Bacterial outer membrane is physiologically shed as bounding membrane of outer membrane vesicles in cultures, as well as in animal tissues at the host-pathogen interface, implicated in translocation of gram-negative microbial biochemical signals to host or target cells.
The biogenesis of the outer membrane requires that the individual components are transported from the site of synthesis to their final destination outside the inner membrane by crossing both hydrophilic and hydrophobic compartments. The machinery and the energy source that drive this process are not yet fully understood. The lipid A-core moiety and the O-antigen repeat units are synthesized at the cytoplasmic face of the inner membrane and are separately exported via two independent transport systems, namely, the O-antigen transporter Wzx (RfbX) and the ATP binding cassette (ABC) transporter MsbA that flips the lipid A-core moiety from the inner leaflet to the outer leaflet of the inner membrane. O-antigen repeat units are then polymerised in the periplasm by the Wzy polymerase and ligated to the lipid A-core moiety by the WaaL ligase.
The LPS transport machinery is composed of LptA, LptB, LptC, LptD, LptE. This supported by the fact that depletion of any one of these proteins blocks the LPS assembly pathway and results in very similar outer membrane biogenesis defects. Moreover, the location of at least one of these five proteins in every cellular compartment suggests a model for how the LPS assembly pathway is organised and ordered in space.
LptC is required for the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane. LptE forms a complex with LptD, which is involved in the assembly of LPS in the outer leaflet of the outer membrane and is essential for envelope biogenesis.
- van der Ley P, Heckels JE, Virji M, Hoogerhout P, Poolman JT (September 1991). "Topology of outer membrane porins in pathogenic Neisseria spp". Infection and immunity 59 (9): 2963–71. PMC 258120. PMID 1652557.
- Feldman MF, Marolda CL, Monteiro MA, Perry MB, Parodi AJ, Valvano MA (December 1999). "The activity of a putative polyisoprenol-linked sugar translocase (Wzx) involved in Escherichia coli O antigen assembly is independent of the chemical structure of the O repeat". J. Biol. Chem. 274 (49): 35129–38. doi:10.1074/jbc.274.49.35129. PMID 10574995.
- Liu D, Cole RA, Reeves PR (April 1996). "An O-antigen processing function for Wzx (RfbX): a promising candidate for O-unit flippase". J. Bacteriol. 178 (7): 2102–7. PMC 177911. PMID 8606190.
- Doerrler WT, Reedy MC, Raetz CR (April 2001). "An Escherichia coli mutant defective in lipid export". J. Biol. Chem. 276 (15): 11461–4. doi:10.1074/jbc.C100091200. PMID 11278265.
- Polissi A, Georgopoulos C (June 1996). "Mutational analysis and properties of the msbA gene of Escherichia coli, coding for an essential ABC family transporter". Mol. Microbiol. 20 (6): 1221–33. doi:10.1111/j.1365-2958.1996.tb02642.x. PMID 8809774.
- Zhou Z, White KA, Polissi A, Georgopoulos C, Raetz CR (May 1998). "Function of Escherichia coli MsbA, an essential ABC family transporter, in lipid A and phospholipid biosynthesis". J. Biol. Chem. 273 (20): 12466–75. doi:10.1074/jbc.273.20.12466. PMID 9575204.
- Raetz CR, Whitfield C (2002). "Lipopolysaccharide endotoxins". Annu. Rev. Biochem. 71: 635–700. doi:10.1146/annurev.biochem.71.110601.135414. PMC 2569852. PMID 12045108.
- Sperandeo P, Lau FK, Carpentieri A, De Castro C, Molinaro A, Deho G, Silhavy TJ, Polissi A (July 2008). "Functional analysis of the protein machinery required for transport of lipopolysaccharide to the outer membrane of Escherichia coli". J. Bacteriol. 190 (13): 4460–9. doi:10.1128/JB.00270-08. PMC 2446812. PMID 18424520.
- Wu T, McCandlish AC, Gronenberg LS, Chng SS, Silhavy TJ, Kahne D (August 2006). "Identification of a protein complex that assembles lipopolysaccharide in the outer membrane of Escherichia coli". Proc. Natl. Acad. Sci. U.S.A. 103 (31): 11754–9. doi:10.1073/pnas.0604744103. PMC 1544242. PMID 16861298.
- Bos MP, Tefsen B, Geurtsen J, Tommassen J (June 2004). "Identification of an outer membrane protein required for the transport of lipopolysaccharide to the bacterial cell surface". Proc. Natl. Acad. Sci. U.S.A. 101 (25): 9417–22. doi:10.1073/pnas.0402340101. PMC 438991. PMID 15192148.
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Lipopolysaccharide-assembly Provide feedback
LptE (formerly known as RplB) is involved in lipopolysaccharide-assembly on the outer membrane of Gram-negative organisms. The lipopolysaccharide component of the outer bacterial membrane is transported from its source of origin to the outer membrane by a set of proteins constituting a transport machinery that is made up of LptA, LptB, LptC, LptD, LptE. LptD appears to be anchored in the outer membrane, and LptE forms a complex with it. This part of the machinery complex is involved in the assembly of lipopolysaccharide in the outer leaflet of the outer membrane .
Sperandeo P, Lau FK, Carpentieri A, De Castro C, Molinaro A, Deho G, Silhavy TJ, Polissi A;, J Bacteriol. 2008;190:4460-4469.: Functional analysis of the protein machinery required for transport of lipopolysaccharide to the outer membrane of Escherichia coli. PUBMED:18424520 EPMC:18424520
This tab holds annotation information from the InterPro database.
InterPro entry IPR007485
The cell envelope of Gram-negative bacteria consists of an inner (IM) and an outer membrane (OM) separated by an aqueous compartment, the periplasm, which contains the peptidoglycan layer. The OM is an asymmetric bilayer, with phospholipids in the inner leaflet and lipopolysaccharides (LPS) facing outward [PUBMED:12045108, PUBMED:16357861]. The OM is an effective permeability barrier that protects the cells from toxic compounds, such as antibiotics and detergents, thus allowing bacteria to inhabit several different and often hostile environments. LPS is responsible for the permeability properties of the OM. LPS consists of the lipid A moiety (a glucosamine-based phospholipid) linked to the short core oligosaccharide and the distal O-antigen polysaccharide chain. The core oligosaccharide can be further divided into an inner core, composed of 3-deoxy-D-mannooctulosanate (KDO) and heptose, and an outer core, which has a somewhat variable structure. LPS is essential in most Gram-negative bacteria, with the notable exception of Neisseria meningitidis. The biogenesis of the OM implies that the individual components are transported from the site of synthesis to their final destination outside the IM by crossing both hydrophilic and hydrophobic compartments. The machinery and the energy source that drive this process are not yet fully understood. The lipid A-core moiety and the O-antigen repeat units are synthesized at the cytoplasmic face of the IM and are separately exported via two independent transport systems, namely, the O-antigen transporter Wzx (RfbX) [PUBMED:10574995, PUBMED:8606190] and the ATP binding cassette (ABC) transporter MsbA that flips the lipid A-core moiety from the inner leaflet to the outer leaflet of the IM [PUBMED:11278265, PUBMED:8809774, PUBMED:9575204]. O-antigen repeat units are then polymerised in the periplasm by the Wzy polymerase and ligated to the lipid A-core moiety by the WaaL ligase [see, PUBMED:12045108, PUBMED:18424520].
The LPS transport machinery is composed of LptA, LptB, LptC, LptD, LptE. This supported by the fact, that depletion of any of one of these proteins blocks the LPS assembly pathway and results in very similar OM biogenesis defects. Moreover, the location of at least one of these five proteins in every cellular compartment suggests a model for how the LPS assembly pathway is organised and ordered in space [PUBMED:18424520].
LptE forms a complex with LptD, which is involved in the assembly of LPS in the outer leaflet of the outer membrane [PUBMED:16861298, PUBMED:18424520, PUBMED:15192148]. LptE interacts with LptD while this protein is being assembled by the beta-barrel assembly machine [PUBMED:21257909]. In Neisseria, LptE does not have a direct role in LPS transport, suggesting that the Lpt system does not function in a completely conserved manner in all Gram-negative bacteria [PUBMED:21705335].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||outer membrane (GO:0019867)|
|Biological process||Gram-negative-bacterium-type cell outer membrane assembly (GO:0043165)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
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You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Previous IDs:||DUF532; RplB;|
|Number in seed:||486|
|Number in full:||1050|
|Average length of the domain:||151.80 aa|
|Average identity of full alignment:||16 %|
|Average coverage of the sequence by the domain:||84.55 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the LptE domain has been found. There are 16 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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