CACHE Domain Research Articles

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

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.

Genetic association of marbling score with intragenic nucleotide variants at selection signals of the bovine genome

Selection signals of Korean cattle might be attributed largely to artificial selection for meat quality. Rapidly increased intragenic markers of newly annotated genes in the bovine genome would help overcome limited findings of genetic markers associated with meat quality at the selection signals in a previous study. The present study examined genetic associations of marbling score (MS) with intragenic nucleotide variants at selection signals of Korean cattle. A total of 39 092 nucleotide variants of 407 Korean cattle were utilized in the association analysis. A total of 129 variants were selected within newly annotated genes in the bovine genome. Their genetic associations were analyzed using the mixed model with random polygenic effects based on identical-by-state genetic relationships among animals in order to control for spurious associations produced by population structure. Genetic associations of MS were found (P<3.88×10−4) with six intragenic nucleotide variants on bovine autosomes 3 (cache domain containing 1, CACHD1), 5 (like-glycosyltransferase, LARGE), 16 (cell division cycle 42 binding protein kinase alpha, CDC42BPA) and 21 (snurportin 1, SNUPN; protein tyrosine phosphatase, non-receptor type 9, PTPN9; chondroitin sulfate proteoglycan 4, CSPG4). In particular, the genetic associations with CDC42BPA and LARGE were confirmed using an independent data set of Korean cattle. The results implied that allele frequencies of functional variants and their proximity variants have been augmented by directional selection for greater MS and remain selection signals in the bovine genome. Further studies of fine mapping would be useful to incorporate favorable alleles in marker-assisted selection for MS of Korean cattle.

Sinorhizobium meliloti Chemoreceptor McpU Mediates Chemotaxis toward Host Plant Exudates through Direct Proline Sensing

Bacterial chemotaxis is an important attribute that aids in establishing symbiosis between rhizobia and their legume hosts. Plant roots and seeds exude a spectrum of molecules into the soil to attract their bacterial symbionts. The alfalfa symbiont Sinorhizobium meliloti possesses eight chemoreceptors to sense its environment and mediate chemotaxis toward its host. The methyl accepting chemotaxis protein McpU is one of the more abundant S. meliloti chemoreceptors and an important sensor for the potent attractant proline. We established a dominant role of McpU in sensing molecules exuded by alfalfa seeds. Mass spectrometry analysis determined that a single germinating seed exudes 3.72 nmol of proline, producing a millimolar concentration near the seed surface which can be detected by the chemosensory system of S. meliloti. Complementation analysis of the mcpU deletion strain verified McpU as the key proline sensor. A structure-based homology search identified tandem Cache (calcium channels and chemotaxis receptors) domains in the periplasmic region of McpU. Conserved residues Asp-155 and Asp-182 of the N-terminal Cache domain were determined to be important for proline sensing by evaluating mutant strains in capillary and swim plate assays. Differential scanning fluorimetry revealed interaction of the isolated periplasmic region of McpU (McpU40-284) with proline and the importance of Asp-182 in this interaction. Using isothermal titration calorimetry, we determined that proline binds with a Kd (dissociation constant) of 104 μM to McpU40-284, while binding was abolished when Asp-182 was substituted by Glu. Our results show that McpU is mediating chemotaxis toward host plants by direct proline sensing.

A Combination of Glycerol and Manganese Promotes Biofilm Formation in Bacillus subtilis via Histidine Kinase KinD Signaling

The spore-forming bacterium Bacillus subtilis forms matrix-enclosed biofilms in response to environmental cues that to date remain poorly defined. Biofilm formation depends on the synthesis of an extracellular matrix, which is indirectly regulated by the transcriptional regulator Spo0A. The activity of Spo0A depends on its phosphorylation state. The level of phosphorylated Spo0A (Spo0A~P) is controlled by a network of kinases and phosphatases, which respond to environmental and physiological signals. In spite of significant progress in understanding biofilm development, the fundamental question of how cells sense the environmental cues that trigger biofilm formation has largely remained unaddressed. Here, we report that biofilm formation of B. subtilis in LB medium is triggered by a combination of glycerol and manganese (GM). Moreover, LB medium with GM significantly stimulates biofilm-associated sporulation and production of an undefined brown pigment. We further show that transcription of the major operons responsible for matrix production and biofilm formation is dramatically enhanced in response to GM. We also establish that KinD is a principal histidine kinase responsible for sensing the presence of GM exclusively by its extracellular CACHE domain. Finally, we show that GM has a similar biofilm-promoting effect in two related Bacillus species, B. licheniformis and B. cereus, indicating that the biofilm-promoting effect of GM is conserved in Bacillus species.

Shewanella oneidensis MR-1 chemotaxis proteins and electron-transport chain components essential for congregation near insoluble electron acceptors

Shewanella oneidensis MR-1 cells utilize a behaviour response called electrokinesis to increase their speed in the vicinity of IEAs (insoluble electron acceptors), including manganese oxides, iron oxides and poised electrodes [Harris, El-Naggar, Bretschger, Ward, Romine, Obraztsova and Nealson (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 326-331]. However, it is not currently understood how bacteria remain in the vicinity of the IEA and accumulate both on the surface and in the surrounding medium. In the present paper, we provide results indicating that cells that have contacted the IEAs swim faster than those that have not recently made contact. In addition, fast-swimming cells exhibit an enhancement of swimming reversals leading to rapid non-random accumulation of cells on, and adjacent to, mineral particles. We call the observed accumulation near IEAs 'congregation'. Congregation is eliminated by the loss of a critical gene involved with EET (extracellular electron transport) (cymA, SO_4591) and is altered or eliminated in several deletion mutants of homologues of genes that are involved with chemotaxis or energy taxis in Escherichia coli. These genes include chemotactic signal transduction protein (cheA-3, SO_3207), methyl-accepting chemotaxis proteins with the Cache domain (mcp_cache, SO_2240) or the PAS (Per/Arnt/Sim) domain (mcp_pas, SO_1385). In the present paper, we report studies of S. oneidensis MR-1 that lend some insight into how microbes in this group can 'sense' the presence of a solid substrate such as a mineral surface, and maintain themselves in the vicinity of the mineral (i.e. via congregation), which may ultimately lead to attachment and biofilm formation.

A Bacillus subtilis sensor kinase involved in triggering biofilm formation on the roots of tomato plants.

The soil bacterium Bacillus subtilis is widely used in agriculture as a biocontrol agent able to protect plants from a variety of pathogens. Protection is thought to involve the formation of bacterial communities - biofilms - on the roots of the plants. Here we used confocal microscopy to visualize biofilms on the surface of the roots of tomato seedlings and demonstrated that biofilm formation requires genes governing the production of the extracellular matrix that holds cells together. We further show that biofilm formation was dependent on the sensor histidine kinase KinD and in particular on an extracellular CACHE domain implicated in small molecule sensing. Finally, we report that exudates of tomato roots strongly stimulated biofilm formation ex planta and that an abundant small molecule in the exudates, (L) -malic acid, was able to stimulate biofilm formation at high concentrations in a manner that depended on the KinD CACHE domain. We propose that small signalling molecules released by the roots of tomato plants are directly or indirectly recognized by KinD, triggering biofilm formation.

Identification of a CACNA2D4 deletion in late onset bipolar disorder patients and implications for the involvement of voltage‐dependent calcium channels in psychiatric disorders

The GWAS-based association of CACNA1C with bipolar disorder (BPD) is one of the strongest genetic findings to date. CACNA1C belongs to the family of CACN genes encoding voltage-dependent calcium channels (VDCCs). VDCCs are involved in brain circuits and cognitive processes implicated in BPD and schizophrenia (SZ). Recently, it was shown that rare copy number variations (CNVs) are found at an increased frequency in SZ and to a lesser extent also in BPD, suggesting the involvement of CNVs in the causation of these diseases. We hypothesize that CNVs in CACN genes can influence the susceptibility to BPD, SZ, and/or schizoaffective disorder (SZA). A search for CNVs in eight CACN genes in a patient-control sample of European decent was performed. A total of 709 BP patients, 645 SZ patients, 189 SZA patients, and 1,470 control individuals were screened using the Multiplex Amplicon Quantification (MAQ) method. We found a rare, partial deletion of 35.7 kb in CACNA2D4 in two unrelated late onset bipolar I patients and in one control individual. All three deletions shared the same breakpoints removing exons 17-26 of CACNA2D4, comprising part of the CACHE domain. Based on the data we cannot claim causality to BPD of the identified CACNA2D4 deletion but nevertheless this deletion can be important in unraveling the underlying processes leading to psychiatric diseases in general and BPD in particular.

Cache-Aware Virtual Machine Scheduling on Multi-Core Architecture

Facing practical limits to increasing processor frequencies, manufacturers have resorted to multi-core designs in their commercial products. In multi-core implementations, cores in a physical package share the last-level caches to improve inter-core communication. To efficiently exploit this facility, operating systems must employ cache-aware schedulers. Unfortunately, virtualization software, which is a foundation technology of cloud computing, is not yet cache-aware or does not fully exploit the locality of the last-level caches. In this paper, we propose a cache-aware virtual machine scheduler for multi-core architectures. The proposed scheduler exploits the locality of the last-level caches to improve the performance of concurrent applications running on virtual machines. For this purpose, we provide a space-partitioning algorithm that migrates and clusters communicating virtual CPUs (VCPUs) in the same cache domain. Second, we provide a time-partitioning algorithm that co-schedules or schedules in sequence clustered VCPUs. Finally, we present a theoretical analysis that proves our scheduling algorithm is more efficient in supporting concurrent applications than the default credit scheduler in Xen. We implemented our virtual machine scheduler in the recent Xen hypervisor with para-virtualized Linux-based operating systems. We show that our approach can improve performance of concurrent virtual machines by up to 19% compared to the credit scheduler.

Two-Component Systems and Their Co-Option for Eukaryotic Signal Transduction

Two-component signaling pathways involve histidine kinases, response regulators, and sometimes histidine-containing phosphotransfer proteins. Prevalent in prokaryotes, these signaling elements have also been co-opted to meet the needs of signal transduction in eukaryotes such as fungi and plants. Here we consider the evolution of such regulatory systems, with a particular emphasis on the roles they play in signaling by the plant hormones cytokinin and ethylene, in phytochrome-mediated perception of light, and as integral components of the circadian clock.

Unexpected chemoreceptors mediate energy taxis towards electron acceptors in Shewanella oneidensis

Shewanella oneidensis uses a wide range of terminal electron acceptors for respiration. In this study, we show that the chemotactic response of S. oneidensis to anaerobic electron acceptors requires functional electron transport systems. Deletion of the genes encoding dimethyl sulphoxide and trimethylamine N-oxide reductases, or inactivation of these molybdoenzymes as well as nitrate reductase by addition of tungstate, abolished electron acceptor taxis. Moreover, addition of nigericin prevented taxis towards trimethylamine N-oxide, dimethyl sulphoxide, nitrite, nitrate and fumarate, showing that this process depends on the DeltapH component of the proton motive force. These data, together with those concerning response to metals (Bencharit and Ward, 2005), support the idea that, in S. oneidensis, taxis towards electron acceptors is governed by an energy taxis mechanism. Surprisingly, energy taxis in S. oneidensis is not mediated by the PAS-containing chemoreceptors but rather by a chemoreceptor (SO2240) containing a Cache domain. Four other chemoreceptors also play a minor role in this process. These results indicate that energy taxis can be mediated by new types of chemoreceptors.

Does the voltage‐gated calcium channel α2δ‐1 subunit play a dual function in skeletal muscle?

The dihydropyridine receptor (DHPR), a high voltage-activated calcium (Ca2+) channel, represents a key element in the excitation–contraction (EC) coupling machinery of muscle cells. In skeletal muscle, the DHPR fulfils two known functions: (i) it controls the ryanodine receptor activity, which makes it commonly referred to as the voltage-sensor for EC coupling and (ii) it supports an L-type voltage-activated Ca2+ current. The DHPR is a macromolecular complex composed of the Cav1.1 pore-forming subunit, surrounded by β1a, γ1 and α2δ-1 auxiliary subunits. Whereas knock-out animals have clearly demonstrated the essential role of Cav1.1 and β1a subunits in EC coupling and in the control of the Ca2+ conductance, the functional importance of α2δ-1 in skeletal muscle remains largely elusive, despite the lethal phenotype of α2δ-1-null embryos. Interestingly, down-regulation of the α2δ-1 protein in the BC3H1 muscle cell line with siRNA only resulted in acceleration of Ca2+ current activation kinetics with no effect on both EC coupling and Cav1.1 trafficking (Obermair et al. 2005). However, it is hard to understand how alteration of Ca2+ current kinetics could be the cause of the lethal phenotype observed in α2δ-1-null mice embryos; instead α2δ-1 is most likely to be involved in other cell functions independent of the DHPR activity. Previous observations suggested such a function: (i) α2δ-1 appears early during muscle development, at a period when the Cav1.1 subunit is not yet expressed, and (ii) sequence analysis of α2δ-1 revealed the presence of consensus domains, known to be involved in cell adhesion and protein–protein interactions (see Fig. 1 for structural organization of the α2δ-1 subunit). In a recent issue of The Journal of Physiology, Garcia et al. raised the possibility that α2δ-1 could mediate the interaction of muscle cells with the extracellular matrix (Garcia et al. 2008). Using immunohistochemistry and a siRNA knock-down strategy, the authors provided new insights into the functional involvement of α2δ-1 in skeletal muscle cells.

Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels

Acetylcholine receptor type ligand-gated ion channels are well known in animals. Homologs are identified in prokaryotes that may act as chemotactic receptors.

MisSPECulation

A majority of the papers published in leading computer architecture conferences use SPEC CPU2000, or its predecessor SPEC CPU95, which has become the de facto standard for measuring processor and/or memory-hierarchy performance. However, in most cases a subset of the suite's benchmarks are simulated. For example: 27 papers were published in ISCA 2002, 16 used SPEC CINT2000, 4 used the whole suite, and only 3 papers explained their omissions.This paper quantifies the extent of this phenomenon in the ISCA, Micro, and HPCA conferences: 173 papers were surveyed, 115 used benchmarks from SPEC CINT, but only 23 used the whole suite. If this current trend continues, by the year 2005 80% of the papers will use the full CINT2000 suite, a year after CPU2004 shall be announced.We claim that results based upon a subset of a benchmark suite are speculative and conflict with Amdahl's Law. The law implies that we must present the speedup of using the proposed technique on the whole suite. Projecting the law (by statistically supplying values for the missing benchmarks) to several published papers reduces promising results to average ones. Speedups are reduced from 1.42 to 1.16 in one case, from 1.43 to 1.13 in another, and from 1.76 to 1.15 in a third.Finally, we have found that the disregard for CFP2000 is unwarranted in papers that explore the data cache domain, the suite displays a higher data cache miss rate than CINT2000, which is used more frequently.