Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

Advances in mass spectrometry-based proteomics have yielded a substantial mapping of the tyrosine phosphoproteome and thus provided an important step toward a systematic analysis of intracellular signaling networks in higher eukaryotes. In this study we decomposed an uncharacterized proteomics data set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified and validated as a binding motif for the SH2 domain-containing inositol phosphatase SHIP2. Our decomposition of the in vivo Tyr(P) proteome furthermore suggests that two-thirds of the Tyr(P) sites mediate interaction, whereas the remaining third govern processes such as enzyme activation and nucleic acid binding.     

Identification of proteins interacting with Arabidopsis ACD11

The Arabidopsis ACD11 gene encodes a sphingosine transfer protein and was identified by the accelerated cell death phenotype of the loss of function acd11 mutant, which exhibits heightened expression of genes involved in the disease resistance hypersensitive response (HR). We used ACD11 as bait in a yeast two-hybrid screen of an Arabidopsis cDNA library to identify ACD11 interacting proteins. One interactor identified is a protein of unknown function with an RNA recognition motif (RRM) designated BPA1 (binding partner of ACD11). Co-immunoprecipitation experiments confirmed the ACD11-BPA1 interactions in vivo and in vitro. Two other ACD11 interactors (PRA7 and PRA8) are homologous to each other and to mammalian PRA1, and both were subsequently shown to interact with BPA1 in yeast. A fourth interactor (VAP27-1) is homologous to mammalian VAP-A, and was found to interact more strongly with a homolog of ACD11 than ACD11 itself. All interactors were shown to be associated with membrane fractions, suggesting that ACD11 function could be related to the regulation of membrane compartments.     

Higher-level phylogenetics of linyphiid spiders (Araneae, Linyphiidae) based on morphological and molecular evidence

This study infers the higher-level cladistic relationships of linyphiid spiders from five genes (mitochondrial CO1, 16S; nuclear 28S, 18S, histone H3) and morphological data. In total, the character matrix includes 47 taxa: 35 linyphiids representing the currently used subfamilies of Linyphiidae (Stemonyphantinae, Mynogleninae, Erigoninae, and Linyphiinae (Micronetini plus Linyphiini)) and 12 outgroup species representing nine araneoid families (Pimoidae, Theridiidae, Nesticidae, Synotaxidae, Cyatholipidae, Mysmenidae, Theridiosomatidae, Tetragnathidae, and Araneidae). The morphological characters include those used in recent studies of linyphiid phylogenetics, covering both genitalic and somatic morphology. Different sequence alignments and analytical methods produce different cladistic hypotheses. Lack of congruence among different analyses is, in part, due to the shifting placement of Labulla , Pityohyphantes , Notholepthyphantes , and Pocobletus . Almost all combined analyses agree on the monophyly of linyphioids, Pimoidae, Linyphiidae, Erigoninae, Mynogleninae, as well as Stemonyphantes as a basal lineage within Linyphiidae. Our results suggest independent origins of the desmitracheate tracheal system in micronetines and erigonines, and that erigonines were primitively haplotracheate. Cephalothoracic glandular specializations of erigonines and mynoglenines apparently evolved independently. Subocular sulci of mynoglenines and lateral sulci (e.g. Bathyphantes ) evolved independently but glandular pores in the prosoma proliferated once. The contribution of different character partitions and their sensitivity to changes in traditional analytical parameters is explored and quantified.
 © The Willi Hennig Society 2009.     

NetPhosBac – A predictor for Ser/Thr phosphorylation sites in bacterial proteins

There is ample evidence for the involvement of protein phosphorylation on serine/threonine/tyrosine in bacterial signaling and regulation, but very few exact phosphorylation sites have been experimentally determined. Recently, gel‐free high accuracy MS studies reported over 150 phosphorylation sites in two bacterial model organisms Bacillus subtilis and Escherichia coli. Interestingly, the analysis of these phosphorylation sites revealed that most of them are not characteristic for eukaryotic‐type protein kinases, which explains the poor performance of eukaryotic data‐trained phosphorylation predictors on bacterial systems. We used these large bacterial datasets and neural network algorithms to create the first bacteria‐specific protein phosphorylation predictor: NetPhosBac. With respect to predicting bacterial phosphorylation sites, NetPhosBac significantly outperformed all benchmark predictors. Moreover, NetPhosBac predictions of phosphorylation sites in E. coli proteins were experimentally verified on protein and site‐specific levels. In conclusion, NetPhosBac clearly illustrates the advantage of taxa‐specific predictors and we hope it will provide a useful asset to the microbiological community.     

Initial effects of experimental warming on carbon exchange rates, plant growth and microbial dynamics of a lichen-rich dwarf shrub tundra in Siberia

Biological soil crusts can affect seed germination and seedling establishment. We have investigated the effect of biological soil crusts on seed water status as a potential mechanism affecting seed germination. The seed water potential of two annual grasses, one exotic Bromus tectorum L. and another native Vulpia microstachys Nutt., were analyzed after placing the seeds on bare soil, on a crust that contains various lichens and mosses (mixed crust), or on a crust dominated by the crustose lichen Diploschistes muscorum (Scop.) R. Sant. (Diploschistes crust). Seed water potential and germination were similar on the bare soil and the mixed crust, except for the initial germination of V. microstachys, which was higher on the mixed crust than on the bare soil. For the two grasses studied, seed water potential was significantly higher on the bare soil and mixed crust than on the Diploschistes crust. These differences in water potential correlated with differences in germination, which was much lower on the lichen crust. Experiments were conducted under two watering regimens. Increasing the frequency of watering amplified the differences in seed water potential and germination between the Diploschistes crust and the other two surfaces. For a particular watering regimen, the bare soil, mixed crust, and Diploschistes crust received the same amount of water, but they reached significantly different water potentials. Throughout the experiments, the water potential of the soil and mixed crust remained above −0.6 MPa, while there was a marked decline in the water potential of the Diploschistes surface to about −4 MPa. To ascertain that water was the major factor limiting germination on the Diploschistes crust, we conducted germination tests in an environment with 100% relative humidity. Under these conditions, germination on the Diploschistes crust was similar to that on the bare soil. However, the seeds that germinated on the Diploschistes crust did not penetrate this surface and approximately 60% of their root tips became necrotic. Our results indicate that the presence of D. muscorum can inhibit seedling establishment by two mechanisms: a reduction in seed water absorption and an increase in root tip mortality.     

Evidence for a host role in regulating the activity of transposable elements in Drosophila melanogaster: the case of the persistent instability of Bari 1 elements in Charolles stock

In most reports in which the activity of numerous Drosophila transposon families has been studied, only a subset of the families tested appears mobile. A comparison of these data shows that there are no transposons inherently more unstable than others and suggests that host factors regulate the activity of transposable elements. Consistent with this conclusion are the properties of Bari 1 elements, which are the only ones of the 14 families tested to be unstable in Charolles stock. Instability is persistent over 53 generations and appears to affect recurrent insertion sites. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genomic distribution of copia-like elements in laboratory stocks of Drosophila melanogaster

The genomic location of five copia-like transposable elements has been compared by the Southern technique in laboratory lines of Oregon R and Canton S strains of Drosophila melanogaster. The results show that extensive rearrangements have taken place in the few decades of separation between the stocks and suggest that transposition occurs at a sizable rate.