Identification of peptidases in Nicotiana tabacum leaf intercellular fluid

Peptidases in the extracellular space might affect the integrity of recombinant proteins expressed in, and secreted from, plant cells. To identify extracellular peptidases, we recovered the leaf intercellular fluid from Nicotiana tabacum plants by an infiltration-centrifugation method. The activity of various peptidases was detected by an in vitro assay in the presence of specific inhibitors, using BSA and human serum gamma-globulin as substrates. Peptidases were detected by 1- and 2-D zymography in a polyacrylamide gel containing gelatin as substrate. Proteolytic activity was observed over a wide range of molecular masses equal to, or higher than, 45 kDa. To identify the peptidases, the extracellular proteins were digested with trypsin and analyzed by LC and MS. Seventeen peptides showing identity or similarity to predicted plant aspartic, cysteine, and serine peptidases have been identified. The extracellular localization of a cysteine peptidase aleurain homolog was also shown.     

Regulation of the high affinity IgE receptor (Fc epsilonRI) in human neutrophils: role of seasonal allergen exposure and Th-2 cytokines

The high affinity IgE receptor, Fc epsilonRI, plays a key role in the immunological pathways involved in allergic asthma. Previously we have demonstrated that human neutrophils isolated from allergic asthmatics express a functional Fc epsilonRI, and therefore it was of importance to examine the factors regulating its expression. In this study, we found that neutrophils from allergic asthmatics showed increased expression of Fc epsilonRI-alpha chain surface protein, total protein and mRNA compared with those from allergic non asthmatics and healthy donors (p<0.001). Interestingly, in neutrophils isolated from allergic asthmatics, Fc epsilonRI-alpha chain surface protein and mRNA expression were significantly greater during the pollen season than outside the pollen season (n = 9, P = 0.001), an effect which was not observed either in the allergic non asthmatic group or the healthy donors (p>0.05). Allergen exposure did not affect other surface markers of neutrophils such as CD16/Fc gammaRIII or IL-17R. In contrast to stimulation with IgE, neutrophils incubated with TH2 cytokines IL-9, GM-CSF, and IL-4, showed enhanced Fc epsilonRI-alpha chain surface expression. In conclusion, these results suggest that enhanced Fc epsilonRI expression in human neutrophils from allergic asthmatics during the pollen season can make them more susceptible to the biological effects of IgE, providing a possible new mechanism by which neutrophils contribute to allergic asthma.     

Bovine hemoglobin: an attractive source of antibacterial peptides

A peptic hemoglobin hydrolysate was fractioned by a semi-preparative reversed-phase HPLC and some fractions have an antibacterial activity against four bacteria strains: Micrococcus luteus A270, Listeria innocua, Escherichia coli and Salmonella enteritidis. These fractions were analyzed by ESI/MS and ESI/MS/MS, in order to characterize the peptides in these fractions. Each fraction contains at least three peptides and some fractions contain five peptides. All these fractions were purified several times by HPLC to obtain pure peptides. Thirty antibacterial peptides were identified. From the isolated antibacterial peptides, 24 peptides were derived from the chains of hemoglobin and 6 peptides were derived from the β chains of hemoglobin. The lowest concentration of these peptides (minimum inhibitory concentration (MIC)) necessary to completely inhibit the growth of four bacteria strain was determined. The cell population of all of the tested bacteria species decreased by at least 97% after a 24-h incubation with any of the peptides at the minimum inhibitory concentration.     

Depletion of beta-COP reveals a role for COP-I in compartmentalization of secretory compartments and in biosynthetic transport of caveolin-1

We have utilized small interfering RNA (siRNA)-mediated depletion of the beta-COP subunit of COP-I to explore COP-I function in organellar compartmentalization and protein traffic. Reduction in beta-COP levels causes the colocalization of markers for the endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC), Golgi, trans-Golgi network (TGN), and recycling endosomes in large, globular compartments. The lack of spatial differentiation of these compartments is not due to a general collapse of all cellular organelles since markers for the early endosomes and lysosomes do not redistribute to the common structures. Anterograde trafficking of the transmembrane cargo vesicular stomatitis virus membrane glycoprotein and of a subset of soluble cargoes is arrested within the common globular compartments. Similarly, recycling traffic of transferrin through the common compartment is perturbed. Furthermore, the trafficking of caveolin-1 (Cav1), a structural protein of caveolae, is arrested within the globular structures. Importantly, Cav1 coprecipitates with the gamma-subunit of COP-I, suggesting that Cav1 is a COP-I cargo. Our findings suggest that COP-I is required for the compartmentalization of the ERGIC, Golgi, TGN, and recycling endosomes and that COP-I plays a novel role in the biosynthetic transport of Cav1.     

Abundance and Production of Riparian Trees in the Lowland Floodplain of the Queets River, Washington

Riparian zones associated with alluvial rivers are spatially dynamic, forming distinct vegetative mosaics that exhibit sharp contrasts in structure and processes related to the underlying biophysical template. The productivity of riparian plants, especially trees, influences streamside community characteristics as well as the forms and fluxes of organic matter to adjacent streams – thereby strongly impacting patterns of channel morphology, water flow, sedimentation, and habitat in rivers. As part of a comprehensive investigation of riparian dynamics in coastal rain forest rivers of the Pacific Northwest (USA), we examined riparian tree abundance (density, basal area, and biomass) and rates of production (basal area growth [BAI] and bole wood biomass increase [P]) of seven common species – red alder (Alnus rubra), Sitka spruce (Picea sitchensis), bigleaf maple (Acer macrophyllum), western hemlock (Tsuga heterophylla), black cottonwood (Populus trichocarpa), vine maple (Acer circinatum) and willow (Salix spp.) – in the lowland floodplain of the Queets River (Olympic National Park), Washington. Measurements were made annually for three years (1999 – 2001) in 16 permanent plots on three biophysical templates that formed a toposequence – active floodplain, young terrace and mature terrace. Stem density was highest in the active floodplain (∼27,000 stems/ ha), decreasing in the young terrace (∼2,700 stems /ha) and the mature terrace (∼500 stems/ha). Basal area and total stem biomass were lowest in the active floodplain (∼16 m2/ha and ∼18 Mg dry weight/ha, respectively) and higher on the young terrace (∼32 m2/ha and ∼134 Mg dry weight/ha) and on the mature terrace (∼69 m2/ha and ∼540 Mg dry weight /ha). Total plot-scale BAI was not significantly different among the physical templates with mean values ranging from approximately 1.4 (low terrace) to approximately 2.8 m2/ha/y (active floodplain). In contrast, P was significantly higher on the mature terrace (10.3 Mg/ha) than the active floodplain (3.2 Mg/ha) but there was no significant difference between young terrace (6.5 Mg/ha) and mature terrace. For the entire Queets River floodplain (57 km² over 77 km of river length), the mature terrace contributed 81% of the total annual production (28,764 Mg) whereas the active floodplain and young terrace accounted only for 5 and 14%, respectively. Overall, we show that riparian trees grow quickly in this coastal Pacific Northwest system and that the older riparian forests on mature terraces are the main contributors to stem production at the plot and floodplain scales for at least 350 years after stand initiation. This suggests that, in combination with the rapid lateral migrations of many alluvial rivers, the older riparian forests on those terraces are important and sustained sources of organic matter (especially large woody debris, LWD) that, over decades to centuries, shape the character of coastal rivers in the Pacific Northwest.     

Assessment of some tools for the characterization of the human osteoarthritic cartilage proteome.

Since the proteome of osteoarthritic articular cartilage has been poorly investigated as yet, we adapted proteomic technologies to the study of the proteins secreted or released by fresh human osteoarthritic cartilage in culture. Fresh cartilage explants were obtained from three donors undergoing surgery for knee joint replacement. The explants were dissected out, minced, and incubated in serum-free culture medium. After 48 h, proteins in the medium were identified by two-dimensional or off-gel electrophoresis coupled to tandem mass spectrometry, or by using an antibody-based protein microarray designed to detect angiogenic factors, growth factors, chemokines, and cytokines. We identified a series of 43 proteins. Some of these proteins were already described as secretion products of chondrocytes, such as YKL-39 or osteoprotegerin, while several other were known proteins but have never been reported previously in cartilage, such as the serum amyloid P-component, the vitamin D binding protein, the pigment epithelium derived factor, the pulmonary and activation-regulated chemokine, lyl-1, thrombopoietin, fibrinogen, angiogenin, gelsolin, and osteoglycin/mimecan. While this study enabled the identification of novel proteins secreted or released by human osteoarthritic cartilage, the goal of the present work was essentially to describe the technical approach necessary for a systematic study of osteoarthritic cartilages from a large population of donors, in order to be able to select the good markers and/or targets for this poorly explored disease.     

Low temperature induces the delivery of mature and immature CFTR to the plasma membrane

Deletion of phenylalanine 508 (ΔF508) is the most prevalent disease-causing mutation resulting in retention of the immature CFTR in the endoplasmic reticulum. The most common strategy to induce the delivery of ΔF508-CFTR to the surface of cells is by reducing the incubation temperature (≈28 °C). Cell surface biotinylation of HEK293T cells grown at 37 °C for 48 h, confirmed the presence of mature wild-type CFTR, but not ΔF508-CFTR at the cell surface. On the other hand, cells incubated at 28 °C for 16 h showed both mature and immature ΔF508-CFTR at their surface. The trafficking of immature ΔF508-CFTR, but not mature ΔF508-CFTR, to the cell surface occurred at low temperature even upon addition of BFA, suggesting the involvement of a Golgi-independent pathway. These results suggest that low temperature induces the appearance of a mix population of mature and immature CFTR molecules at the plasma membrane through distinct pathways.     

Identification and functional expression of a second human beta-galactoside alpha2,6-sialyltransferase, ST6Gal II.

BLAST analysis of the human and mouse genome sequence databases using the sequence of the human CMP-sialic acid:beta-galactoside alpha-2,6-sialyltransferase cDNA (hST6Gal I, EC2.4.99.1) as a probe allowed us to identify a putative sialyltransferase gene on chromosome 2. The sequence of the corresponding cDNA was also found as an expressed sequence tag of human brain. This gene contained a 1590 bp open reading frame divided in five exons and the deduced amino-acid sequence didn't correspond to any sialyltransferase already known in other species. Multiple sequence alignment and subsequent phylogenic analysis showed that this new enzyme belonged to the ST6Gal subfamily and shared 48% identity with hST6Gal-I. Consequently, we named this new sialyltransferase ST6Gal II. A construction in pFlag vector transfected in COS-7 cells gave raise to a soluble active form of ST6Gal II. Enzymatic assays indicate that the best acceptor substrate of ST6Gal II was the free disaccharide Galbeta1-4GlcNAc structure whereas ST6Gal I preferred Galbeta1-4GlcNAc-R disaccharide sequence linked to a protein. The alpha2,6-linkage was confirmed by the increase of Sambucus nigra agglutinin-lectin binding to the cell surface of CHO transfected with the cDNA encoding ST6Gal II and by specific sialidases treatment. In addition, the ST6Gal II gene showed a very tissue specific pattern of expression because it was found essentially in brain whereas ST6Gal I gene is ubiquitously expressed.