Mechanism of persistent protein kinase D1 translocation and activation

The specificity of many signal transduction pathways relies on the spatiotemporal features of each signaling step. G protein-coupled receptor-mediated activation of protein kinases leads to diverse cellular effects. Upon receptor activation, PKD1 and several C-type protein kinases (PKCs), translocate to the plasma membrane and become catalytically active. Here we show that, unlike PKCs, PKD1 remains active at the membrane for hours. The two DAG binding C1 domains of PKD1 have distinct functional roles in targeting and maintaining PKD1 at the plasma membrane. C1A achieves fast, maximal, and reversible translocation, while C1B translocates partially, but persistently, to the plasma membrane. The persistent localization requires the C1B domain of PKD1, which binds Galphaq. We incorporate the kinetics of PKD1 translocation into a three-state model that suggests how PKD1 binding to DAG and Galphaq uniquely encodes frequency-dependent PKD1 signaling.     

Expression of peripheral benzodiazepine receptor (PBR) in human tumors: relationship to breast, colorectal, and prostate tumor progression

High levels of peripheral-type benzodiazepine receptor (PBR), the alternative-binding site for diazepam, are part of the aggressive human breast cancer cell phenotype in vitro. We examined PBR levels and distribution in normal tissue and tumors from multiple cancer types by immunohistochemistry. Among normal breast tissues, fibroadenomas, primary and metastatic adenocarcinomas, there is a progressive increase in PBR levels parallel to the invasive and metastatic ability of the tumor (p < 0.0001). In colorectal and prostate carcinomas, PBR levels were also higher in tumor than in the corresponding non-tumoral tissues and benign lesions (p < 0.0001). In contrast, PBR was highly concentrated in normal adrenal cortical cells and hepatocytes, whereas in adrenocortical tumors and hepatomas PBR levels were decreased. Moreover, malignant skin tumors showed decreased PBR expression compared with normal skin. These results indicate that elevated PBR expression is not a common feature of aggressive tumors, but rather may be limited to certain cancers, such as those of breast, colon-rectum and prostate tissues, where elevated PBR expression is associated with tumor progression. Thus, we propose that PBR overexpression could serve as a novel prognostic indicator of an aggressive phenotype in breast, colorectal and prostate cancers.     

Mapping functional associations in the entire genome of Drosophila melanogaster using fusion analysis

We have previously shown that the detection of gene fusion events can contribute towards the elucidation of functional associations of proteins within entire genomes. Here we have analysed the entire genome of Drosophila melanogaster using fusion analysis and two additional constraints that improve the reliability of the predictions, viz. low sequence similarity and low degree of paralogy of the component proteins involved in a fusion event. Imposing these constraints, the total number of unique component pairs is reduced from 18 654 to a mere 220 cases, which are expected to represent some of the most reliably detected functionally associated proteins. Using additional information from sequence databases, we have been able to detect pairs of functionally associated proteins with important functions in cellular and developmental pathways, such as spermatogenesis and programmed cell death.     

Lipids of the hexane extract from the roots of medicinal boraginaceous species

The chemical compositions of hexane extracts of the lipid fraction of the roots of the medicinal Boraginaceous species Alkanna tinctoria, Onosma heterophylla, Macrotomia densiflora and Onosma hispidium are presented and their phytochemical relevance evaluated. The predominating fatty acids in all of the root lipids were stearic, palmitic, oleic, linoleic and gamma-linolenic acids, while the latter and stearidonic acid predominated in the seeds and leaves of various Boraginaceous species. The indigenous presence of methyl, ethyl and isopropyl esters of fatty acids, reported for the first time in the roots of higher plants, is considered to be of particular importance in the biosynthesis of fatty substances. The results suggest the use of fatty acids as chemotaxonomic markers for Boraginaceous species and the utilisation of Boraginaceous species as new commercial sources for fatty acids with valuable medicinal and nutritional properties.     

Individual‐based and stochastic modeling of cell population dynamics considering substrate dependency

In this article, we propose an individual‐based and stochastic modeling approach that is capable of describing the bacterial cell population dynamics during a batch culture. All stochastic nature inherent in intracellular molecular level reactions and cell division processes were considered in a single model framework by embedding a sub‐model describing individual cell's growth kinetics in a discrete event simulation algorithm. The resultant unique feature of the model is that the effects of the stochasticities on the cell population dynamics can be investigated for different substrate‐dependent cell growth kinetics. When Monod kinetics was used as the sub‐model, the stochasticities only slightly affected the cell mass increase and substrate consumption profiles during the batch culture although they were still important in describing the changes of cell population distributions. When Andrews substrate inhibition kinetics was used, however, it was revealed that the overall cell population dynamics could be seriously influenced by the stochasticities. Under a critical initial substrate level, the cell population could proliferate against the substrate inhibition only when the stochasticities were considered. Biotechnol. Bioeng. 2009;103: 891–899. © 2009 Wiley Periodicals, Inc.     

Knockdown of aquaporin-8 induces mitochondrial dysfunction in 3T3-L1 cells

BackgroundAquaporin-8 (AQP8), a member of the aquaporin water channel family, is expressed in various tissue and cells, including liver, testis, and pancreas. AQP8 appears to have functions on the plasma membrane and/or on the mitochondrial inner membrane. Mitochondrial AQP8 with permeability for water, H₂O₂ and NH₃ has been expected to have important role in various cells, but its information is limited to a few tissues and cells including liver and kidney. In the present study, we found that AQP8 was expressed in the mitochondria in mouse adipose tissues and 3T3-L1 preadipocytes, and investigated its role by suppressing its gene expression.MethodsAQP8-knocked down (shAQP8) cells were established using a vector expressing short hairpin RNA. Cellular localization of AQP8 was examined by western blotting and immunocytochemistry. Mitochondrial function was assessed by measuring mitochondrial membrane potential, oxygen consumption and ATP level measurements.ResultsIn 3T3-L1 cells, AQP8 was expressed in the mitochondria. In shAQP8 cells, mRNA and protein levels of AQP8 were decreased by about 75%. The shAQP8 showed reduced activities of complex IV and ATP synthase; it is probable that the impaired mitochondrial water handling in shAQP8 caused suppression of the electron transport and ADP phosphorylation through inhibition of the two steps which yield water. The reduced activities of the last two steps of oxidative phosphorylation in shAQP8 cause low routine and maximum capacity of respiration and mitochondrial hyperpolarization.ConclusionMitochondrial AQP8 contributes to mitochondrial respiratory function probably through maintenance of water homeostasis.General significanceThe AQP8-knocked down cells we established provides a model system for the studies on the relationships between water homeostasis and mitochondrial function.     

Inhibition of αIIbβ3 Ligand Binding by an αIIb Peptide that Clasps the Hybrid Domain to the βI Domain of β3

Agonist-stimulated platelet activation triggers conformational changes of integrin αIIbβ3, allowing fibrinogen binding and platelet aggregation. We have previously shown that an octapeptide, ^p1YMESRADR⁸, corresponding to amino acids 313–320 of the β-ribbon extending from the β-propeller domain of αIIb, acts as a potent inhibitor of platelet aggregation. Here we have performed in silico modelling analysis of the interaction of this peptide with αIIbβ3 in its bent and closed (not swing-out) conformation and show that the peptide is able to act as a substitute for the β-ribbon by forming a clasp restraining the β3 hybrid and βI domains in a closed conformation. The involvement of species-specific residues of the β3 hybrid domain (E356 and K384) and the β1 domain (E297) as well as an intrapeptide bond (^pE315-^pR317) were confirmed as important for this interaction by mutagenesis studies of αIIbβ3 expressed in CHO cells and native or substituted peptide inhibitory studies on platelet functions. Furthermore, NMR data corroborate the above results. Our findings provide insight into the important functional role of the αIIb β-ribbon in preventing integrin αIIbβ3 head piece opening, and highlight a potential new therapeutic approach to prevent integrin ligand binding.     

Computation of repetitions and regularities of biologically weighted sequences.

Biological weighted sequences are used extensively in molecular biology as profiles for protein families, in the representation of binding sites and often for the representation of sequences produced by a shotgun sequencing strategy. In this paper, we address three fundamental problems in the area of biologically weighted sequences: (i) computation of repetitions, (ii) pattern matching, and (iii) computation of regularities. Our algorithms can be used as basic building blocks for more sophisticated algorithms applied on weighted sequences.