A Novel Motif Identified in Dependence Receptors

Programmed cell death signaling is a critical feature of development, cellular turnover, oncogenesis, and neurodegeneration, among other processes. Such signaling may be transduced via specific receptors, either following ligand binding—to death receptors—or following the withdrawal of trophic ligands—from dependence receptors. Although dependence receptors display functional similarities, no common structural domains have been identified. Therefore, we employed the Multiple Expectation Maximization for Motif Elicitation and the Motif Alignment and Search Tool software programs to identify a novel transmembrane motif, dubbed dependence-associated receptor transmembrane (DART) motif, that is common to all described dependence receptors. Of 3,465 human transmembrane proteins, 25 (0.7%) display the DART motif. The predicted secondary structure features an alpha helical structure, with an unusually high percentage of valine residues. At least four of the proteins undergo regulated intramembrane proteolysis. To date, we have not identified a function for this putative domain. We speculate that the DART motif may be involved in protein processing, interaction with other proteins or lipids, or homomultimerization

Fall, Recovery and Characterization of the Novato L6 Chondrite Breccia

The Novato L6 chondrite fragmental breccia fell in California on 17 October 2012, and was recovered after the Cameras for Allsky Meteor Surveillance (CAMS) project determined the meteor's trajectory between 95 and 45 km altitude. The final fragmentation at 33 1 km altitude was exceptionally well documented by digital photographs. The first sample was recovered before rain hit the area. First results from a consortium study of the meteorite's characterization, cosmogenic and radiogenic nuclides, origin and conditions of the fall are presented. Some meteorites did not retain fusion crust and show evidence of spallation. Before entry, the meteoroid was 35+/-5 cm in diameter (mass 80+/-35 kg) with a cosmic ray exposure age of 9+/-1 Ma, if it had a one-stage exposure history. However, based on the cosmogenic nuclide inventory, a two-stage exposure history is more likely, with lower shielding in the last few Ma. Thermoluminescence data suggest a collision event within the last approx. 0.1 Ma. Novato likely belonged to the class of shocked L chondrites that have a common shock age of 470 Ma, based on the U,Th-He age of 460+/-220 Ma. The measured orbits of Novato, Jesenice and Innisfree are consistent with a proposed origin of these shocked L chondrites in the Gefion asteroid family, but leave open the possibility that they came to us directly from the 5:2 mean motion resonance with Jupiter. Novato experienced a stronger compaction than did other L6 chondrites of shock-stage S4. Despite this, a freshly broken surface shows a wide range of organic compounds

Ten dependence receptors (plus orthologues) comprise the training set for the MEME query.

<p>Ten dependence receptors plus their orthologues (32 sequences total) were used as a training set by the MEME program to search for high-scoring motifs common to all proteins. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000463#pone-0000463-t001" target="_blank">Table 1</a> shows the transmembrane location (for each protein with one) and the location of the DART motif. Data taken from the Swiss-Prot database. All accession numbers are from Swiss-Prot.</p

16 human proteins found to display the DART motif.

<p>Sixteen human proteins were discovered that display high-scoring matches for the DART motif when the Swiss-Prot database was searched using the MAST software program. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000463#pone-0000463-t003" target="_blank">Table 3</a> shows the transmembrane location and the location of the DART motif. Data taken from the Swiss-Prot database. All accession numbers are from Swiss-Prot.</p

MAST result list of 54 non-training set proteins found to display the DART motif.

<p>The top-scoring non-training-set proteins displaying the DART motif, representing 38 proteins (plus 16 orthologues). Sixteen of the 54 are the human proteins listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000463#pone-0000463-t003" target="_blank">Table 3</a>.</p

Dendrogram of the 26 human DART-containing proteins.

<p>Dendrogram demonstrating the relationships of the DART motif sequences within each of the 26 human proteins found to contain DART (10 from the training set plus 16 discovered through the use of MAST).</p

Predicted secondary structure of the consensus sequence of DART.

<p>SOPMA analysis demonstrates the alpha-helical nature of the putative DART domain.</p

Aligned DART motif within all dependence receptor training set members.

<p>Occurrences (sites) of the DART motif within the sequences of the 32 dependence receptors that were used as the training set. The sites are shown aligned with each other, and the ten sequence positions preceding and following each site are also shown. Each site is identified by the name of the sequence where it occurs and the position in the sequence where the site begins. The sites are listed in order of increasing p-value (decreasing statistical significance). The p-value of a site is computed from the match score of the site with the position specific scoring matrix for the motif. The p-value gives the probability of a random string (generated from the background letter frequencies) having the same match score or higher. Amino acid residues constituting the transmembrane region of the protein are indicated by shading.</p

Multilevel consensus sequence and amino acid frequency of the DART motif.

<p>MEME motifs are represented by position-specific probability matrices that specify the probability of each possible letter appearing at each possible position in an occurrence of the motif. In order to make it easier to see which letters are most likely in each of the columns of the motif, the simplified motif shows the letter probabilities multiplied by 10 rounded to the nearest integer. Zeros are replaced by “:” (a colon) for readability. The information content diagram provides an idea of which positions in the motif are most highly conserved. Each column (position) in a motif can be characterized by the amount of information it contains (measured in bits). Highly conserved positions in the motif have high information; positions where all letters are equally likely have low information. The diagram is printed so that each column lines up with the same column in the simplified position-specific probability matrix above it. This multilevel consensus sequence says several things about the motif. First, the most likely form of the motif can be read from the top line as LLVIAVVVALVIxVLLVxL. Second, that only letter L has probability more than 0.2 in position 1 of the motif, both L and I have probability greater than 0.2 in position 2, etc. Third, a rough approximation of the motif can be made by converting the multilevel consensus sequence into the Prosite signature: L-[LI]-V-I-[AS]-V-V-V-[AGS]-L-V-[IF]-x-[VI]-L-[LV]-V-x-[LI].</p