Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa

In contrast to Escherichia coli, a model organism for chemotaxis that has 5 chemoreceptors and a single chemosensory pathway, Pseudomonas aeruginosa PAO1 has a much more complex chemosensory network, which consists of 26 chemoreceptors feeding into four chemosensory pathways. While several chemoreceptors were rigorously linked to specific pathways in a series of experimental studies, for most of them this information is not available. Thus, we addressed the problem computationally. Protein–protein interaction network prediction, coexpression data mining, and phylogenetic profiling all produced incomplete and uncertain assignments of chemoreceptors to pathways. However, comparative sequence analysis specifically targeting chemoreceptor regions involved in pathway interactions revealed conserved sequence patterns that enabled us to unambiguously link all 26 chemoreceptors to four pathways. Placing computational evidence in the context of experimental data allowed us to conclude that three chemosensory pathways in P. aeruginosa utilize one chemoreceptor per pathway, whereas the fourth pathway, which is the main system controlling chemotaxis, utilizes the other 23 chemoreceptors. Our results show that while only a very few amino acid positions in receptors, kinases, and adaptors determine their pathway specificity, assigning receptors to pathways computationally is possible. This requires substantial knowledge about interacting partners on a molecular level and focusing comparative sequence analysis on the pathway-specific regions. This general principle should be applicable to resolving many other receptor–pathway interactions

Spaces of Yoga – Towards a Non-Essentialist Understanding of Yoga

This chapter will examine some of the spaces that yoga occupies in the contemporary world, both physical and social. By looking at yoga through the focus of particular, contested spaces and locations, it will be argued that overarching essentialist definitions of yoga are impossible, although individuals and social groups can and do create essentialist definitions that are more or less useful for particular purposes. By exploring these narratives and boundaries in the context of specific locations, we can better understand what people are doing with the collection of beliefs and practices known as yoga

Very Low Pressure Plasma Spray—A Review of an Emerging Technology in the Thermal Spray Community

A fundamentally new family of thermal spray processes has emerged. These new processes, collectively known as very low pressure plasma spray or VLPPS, differ from traditional thermal spray processes in that coatings are deposited at unusually low chamber pressures, typically less than ~800 Pa (6 Torr). Depending upon the specific process, deposition may be in the form of very fine molten droplets, vapor phase deposition, or a mixture of vapor and droplet deposition. Resulting coatings are similar in quality to coatings produced by alternative coating technologies, such as physical vapor deposition (PVD) or chemical vapor deposition (CVD), but deposition rates can be roughly an order of magnitude higher with VLPPS. With these new process technologies modified low pressure plasma spray (LPPS) systems can now be used to produce dense, high quality coatings in the 1 to 100 micron thickness range with lamellar or columnar microstructures. A history of pioneering work in VLPPS technology is presented, deposition mechanisms are discussed, potential new applications are reviewed, and challenges for the future are outlined

Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

<div><p>Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly built computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms. Furthermore, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes.</p></div

Relationship between Cache (red), PAS (blue) and GAF (green) superfamilies.

<p>(<b>A</b>) HMM-to-HMM comparisons. The nodes represent domain families. Links represent reciprocal hits in hhsearch. Hits with an E-value <1e-3 are shown as thick lines, those with E-value <1e-1 are shown as thin lines and dotted lines represent hits with >90 probability score. Filled circles represent PAS and GAF domain families that were identified in HHpred search using new Cache models. Families that were not identified in these searches are depicted by empty circles (<b>B</b>) Sequence-to-sequence comparisons. The outer circle represents domain families. Links between individual sequences represent reciprocal BLAST hits with an E-value threshold of 1e-8, the lowest E-value at which no links between superfamilies were found. However, the overall relationships shown here remain at less stringent E-values.</p

Examples of newly identified and better defined Cache domains in diverse signal transduction proteins from bacteria, archaea and eukaryotes.

<p>Domain architectures for representative sequences from model organisms are shown along with their UniProt accession numbers. Newly defined Cache domains are shown in red. Cache boundaries defined by the previous Pfam models are shown in pink (Cache) and green (MCP_N). HAMP domains are shown as grey circles, PAS domains as cyan circles, and HisKA domains as white circles. Other Pfam domains are abbreviated as follows: MCP, MCPsignal; GGDEF, GGDEF; GC, guanylate cyclase; HK, the histidine kinase HATPase_c domian; RR, response regulator; VWA, a combination of VWA_N and VWA domains; VGCC, VGCC_alpha2.</p

Phyletic distribution of PAS (blue), GAF (green) and Cache (red) domains.

<p>Flags at the outer three layers represent the domain presence in a corresponding genome. The tree was built using taxonomic ranks retrieved from NCBI.</p

Comparison of sequence- and structure-based definitions for extracellular PAS-like domains.

<p>(A) <i>Vibrio parahaemolyticus</i> chemoreceptor (PDB: 2QHK); (B) <i>Vibrio cholerae</i> chemoreceptor (PDB: 3C8C). Domains are visualized on sequences with corresponding amino acid positions (top) and structures (bottom). Cache (cyan) domains are defined by Pfam; PAS domains (green and magenta) were defined by visual inspection of corresponding structures.</p

Relative abundance of known extracellular sensory domains in prokaryotes.

<p>Domain counts were obtained by running Pfamscan against a dataset of non-redundant prokaryotic extracellular sequences, which was also used for HMM construction (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004862#sec010" target="_blank">Methods</a>).</p

Length distribution of Cache domains identified using the new domain models.

<p>Results for searches of the Pfam 27.0 associated UniProt database (June 2012 release) using the newly built single and double Cache models and the unchanged YkuI_C model are shown. Shaded areas show the upper and lower boundaries of known single and double Cache domain structures. Outliers represent partial protein sequences as well as partial matches to models (very short sequences) and sequences with large insertions within the Cache domain (very long sequences). See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004862#pcbi.1004862.s018" target="_blank">S2 Data</a> for details.</p