Compressibilities and volume fluctuations of archaeal tetraether liposomes

Bipolar tetraether lipids (BTLs) are abundant in crenarchaeota, which thrive in both thermophilic and nonthermophilic environments, with wide-ranging growth temperatures (4-108°C). BTL liposomes can serve as membrane models to explore the role of BTLs in the thermal stability of the plasma membrane of crenarchaeota. In this study, we focus on the liposomes made of the polar lipid fraction E (PLFE). PLFE is one of the main BTLs isolated from the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. Using molecular acoustics (ultrasound velocimetry and densimetry), pressure perturbation calorimetry, and differential scanning calorimetry, we have determined partial specific adiabatic and isothermal compressibility, their respective compressibility coefficients, partial specific volume, and relative volume fluctuations of PLFE large unilamellar vesicles (LUVs) over a wide range of temperatures (20-85°C). The results are compared with those obtained from liposomes made of dipalmitoyl-L-α-phosphatidylcholine (DPPC), a conventional monopolar diester lipid. We found that, in the entire temperature range examined, compressibilities of PLFE LUVs are low, comparable to those found in gel state of DPPC. Relative volume fluctuations of PLFE LUVs at any given temperature examined are 1.6-2.2 times more damped than those found in DPPC LUVs. Both compressibilities and relative volume fluctuations in PLFE LUVs are much less temperature-sensitive than those in DPPC liposomes. The isothermal compressibility coefficient (β_T^lipid) of PLFE LUVs changes from 3.59 × 10⁻¹⁰ Pa⁻¹ at 25°C to 4.08 × 10⁻¹⁰ Pa⁻¹ at 78°C. Volume fluctuations of PLFE LUVs change only 0.25% from 30°C to 80°C. The highly damped volume fluctuations and their low temperature sensitivity, echo that PLFE liposomes are rigid and tightly packed. To our knowledge, the data provide a deeper understanding of lipid packing in PLFE liposomes than has been previously reported, as well as a molecular explanation for the low solute permeation and limited membrane lateral motion. The obtained results may help to establish new strategies for rational design of stable BTL-based liposomes for drug/vaccine delivery.     

High-pressure SAXS study of folded and unfolded ensembles of proteins

A structural interpretation of the thermodynamic stability of proteins requires an understanding of the structural properties of the unfolded state. High-pressure small-angle x-ray scattering was used to measure the effects of temperature, pressure, denaturants, and stabilizing osmolytes on the radii of gyration of folded and unfolded state ensembles of staphylococcal nuclease. A set of variants with the internal Val-66 replaced with Ala, Tyr, or Arg was used to examine how changes in the volume and polarity of an internal microcavity affect the dimensions of the native state and the pressure sensitivity of the ensemble. The unfolded state ensembles achieved for these proteins with high pressure were more compact than those achieved at high temperature, and were all very sensitive to the presence of urea and glycerol. Substitutions at the hydrophobic core detectably altered the conformation of the protein, even in the folded state. The introduction of a charged residue, such as Arg, inside the hydrophobic interior of a protein could dramatically alter the structural properties, even those of the unfolded state. The data suggest that a charge at an internal position can interfere with the formation of transient hydrophobic clusters in the unfolded state, and ensure that the pressure-unfolded form of a protein occupies the maximum volume possible. Only at high temperatures does the radius of gyration of the unfolded state ensemble approach the value for a statistical random coil.     

Effects of human respiratory syncytial virus, metapneumovirus, parainfluenza virus 3 and influenza virus on CD4+ T cell activation by dendritic cells

BACKGROUND: Human respiratory syncytial virus (HRSV), and to a lesser extent human metapneumovirus (HMPV) and human parainfluenza virus type 3 (HPIV3), re-infect symptomatically throughout life without antigenic change, suggestive of incomplete immunity. One causative factor is thought to be viral interference with dendritic cell (DC)-mediated stimulation of CD4+ T cells. METHODOLOGY, PRINCIPAL FINDINGS: We infected human monocyte-derived DC with purified HRSV, HMPV, HPIV3, or influenza A virus (IAV) and compared their ability to induce activation and proliferation of autologous CD4+ T cells in vitro. IAV was included because symptomatic re-infection without antigenic change is less frequent, suggesting that immune protection is more complete and durable. We examined virus-specific memory responses and superantigen-induced responses by multiparameter flow cytometry. Live virus was more stimulatory than inactivated virus in inducing DC-mediated proliferation of virus-specific memory CD4+ T cells, suggesting a lack of strong suppression by live virus. There were trends of increasing proliferation in the order: HMPV相似文献   

Hydrogen formation by an arsenate-reducing Pseudomonas putida, isolated from arsenic-contaminated groundwater in West Bengal, India

Anaerobic growth of a newly isolated Pseudomonas putida strain WB from an arsenic-contaminated soil in West Bengal, India on glucose, l-lactate, and acetate required the presence of arsenate, which was reduced to arsenite. During aerobic growth in the presence of arsenite arsenate was formed. Anaerobic growth of P. putida WB on glucose was made possible presumably by the non-energy-conserving arsenate reductase ArsC with energy derived only from substrate level phosphorylation. Two moles of acetate were generated intermediarily and the reducing equivalents of glycolysis and pyruvate decarboxylation served for arsenate reduction or were released as H₂. Anaerobic growth on acetate and lactate was apparently made possible by arsenate reductase ArrA coupled to respiratory electron chain energy conservation. In the presence of arsenate, both substrates were totally oxidized to CO₂ and H₂ with part of the H₂ serving for respiratory arsenate reduction to deliver energy for growth. The growth yield for anaerobic glucose degradation to acetate was Y _Glucose = 20 g/mol, leading to an energy coefficient of Y _ATP = 10 g/mol adenosine-5'-triphosphate (ATP), if the Emden–Meyerhof–Parnas pathway with generation of 2 mol ATP/mol glucose was used. During growth on lactate and acetate no substrate chain phosphorylation was possible. The energy gain by reduction of arsenate was Y _Arsenate = 6.9 g/mol, which would be little less than one ATP/mol of arsenate.     

The tangled core at the heart of the bryozoan suborder Phylloporinina

Abstract: The family Phylloporinidae was introduced in the late 19th century to accommodate a small number of Palaeozoic bryozoan genera characterized by irregularly fenestrated colonies generated by anastomosis of unilaminate branches. Among the first named of these genera were Chasmatopora Eichwald, 1855 and Phylloporina Ulrich in Foerste, 1887. The two names have been variously in fashion, and there has been confusion about whether they are subjective synonyms or are distinct genera. This taxonomic confusion has been due in large part to whether the single species (Retepora angulata Hall, 1847) assigned to Phylloporina in Foerste (1887) or the species that Ulrich intended (Retepora trentonensis Nicholson, 1875) is the type species and also because of lack of sufficient information about Foerste’s material to characterize it well. We here redescribe the pertinent species, erect the new species Chasmatopora foerstei for the species that Foerste incorrectly assigned to Phylloporina angulata (Hall), and suggest that Retepora trentonensis Nicholson be retained as type species of Phylloporina based on prevailing usage, until the issue is settled by the International Commission on Zoological Nomenclature.     

The Changing Fate of a Secretory Glycoprotein in Developing Maize Endosperm

Zeins are the major storage proteins in maize (Zea mays) endosperm, and their accumulation in zein bodies derived from the endoplasmic reticulum is well characterized. In contrast, relatively little is known about post-Golgi compartments or the trafficking of vacuolar proteins in maize endosperm, specifically the presence of globulins in structures resembling protein storage vacuoles that appear in early to mid-stage seed development. We investigated this pathway by expressing and analyzing a recombinant reporter glycoprotein during endosperm maturation, using a combination of microscopy and sensitive glycopeptide analysis. Specific N-glycan acceptor sites on the protein were followed through the stages of grain development, revealing a shift from predominantly paucimannosidic vacuolar glycoforms to predominantly trimmed glycan structures lacking fucose. This was accompanied by a change in the main subcellular localization of the protein from large protein storage vacuole-like post-Golgi organelles to the endoplasmic reticulum and zein bodies. The endogenous storage proteins corn α-globulin and corn legumin-1 showed a similar spatiotemporal profile both in transgenic plants expressing the reporter glycoprotein and in wild-type plants. This indicates that the shift of the intracellular trafficking route, as observed with our reporter glycoprotein, may be a common strategy in maize seed development.Storage proteins in cereal seeds accumulate in different compartments of the endosperm cell, and their abundance and distribution varies according to the species. While in most cereals prolamins are the more abundant class of storage proteins, small-grain species (e.g. wheat [Triticum aestivum], oat [Avena sativa], and barley [Hordeum vulgare]) may contain variable proportions of both prolamins and globulins, and these are delivered to the protein storage vacuole (PSV) via Golgi-dependent and Golgi-independent pathways (Wettstein, 1980; Levanony et al., 1992; Herman and Schmidt, 2004; Takahashi et al., 2005; Cameron-Mills and von Tosi et al., 2009). In rice (Oryza sativa), where globulins and prolamins accumulate in distinct storage compartments, most globulins (mainly glutelins) accumulate in PSVs whereas prolamins aggregate into dense protein bodies within the rough endoplasmic reticulum (ER) and remain in ER-derived organelles (Okita and Rogers, 1996). Maize (Zea mays) stores mainly prolamins (zeins) comprised in three zein subfamilies (α, γ, and δ) that form ER-derived zein bodies. Mature zein bodies consist of a central core of α and δ zeins, while γ zeins are mainly found in the periphery (Lending and Larkins, 1989). Small amounts of globulins also accumulate in maize endosperm, i.e. corn α-globulin (CAG) and corn legumin-1 (CL-1; Woo et al., 2001). Unlike legumin homologs in other plant species including cereals, CL-1 lacks the canonical asparaginyl endopeptidase cleavage sequence (Woo et al., 2001), so it is not cleaved into α and β chains (Yamagata et al., 2003). CAG has been observed in small, PSV-like compartments within the maize endosperm cell (Woo et al., 2001) and a similar fate has been predicted for CL-1 (Yamagata et al., 2003). The identification and localization of globulins in maize indicates the presence of storage vacuoles in maize endosperm, but it does not address the question whether the size and number of these organelles is significant in maize, whether they change morphologically during seed maturation, and how proteins reach this destination.Proteins may reach the PSV by different routes, and in some species storage protein trafficking appears to undergo changes during seed development. For example, in the context of 2S and 11S storage protein trafficking in pumpkin (Cucurbita pepo) and castor bean (Ricinus communis) it has been proposed that seed developmental stages may be important in determining the transport routes to the PSV (Vitale and Hinz, 2005). A seed-development-mediated change in the trafficking route of wheat prolamins has been suggested earlier as well (Shy et al., 2001; Tosi et al., 2009). One approach to study such change in trafficking routes along seed maturation is to scrutinize the glycosylation pattern of proteins destined to the PSV, taking advantage of the fact that the intracellular trafficking route of a glycoprotein determines its final N-glycan structures (Lerouge et al., 1998).The first stage of N-glycosylation (which takes place in the ER) involves the cotranslational addition of a precursor oligosaccharide (Glc₃Man₉GlcNAc₂) that is modified by various glycosidases and glycosyltransferases to form the final glycan structure as the protein migrates through the endomembrane system (Lis and Sharon, 1993; Lerouge et al., 1998). ER-resident glycoproteins contain high-Man-type N-glycans whereas proteins passing though the Golgi apparatus contain complex-type N-glycans that include α(1-3)-Fuc and/or β(1-2)-Xyl residues (Lerouge et al., 1998). While secreted glycoproteins contain terminal GlcNAc residues in addition to the core Fuc and Xyl, these terminal residues are trimmed off by enzymes either en route to the vacuole or within the vacuole (Lerouge et al., 1998). Thus the structure of N-glycans is a useful indicator for the intracellular pathway of a protein (Vitale and Hinz, 2005).Unfortunately, most seed storage proteins, particularly those in cereals, are not glycosylated. However, information on N-glycan structures can be obtained from recombinant glycoproteins. For example, a KDEL-tagged antibody, which was located primarily in ER-derived zein bodies, was predominantly made up of molecules with single GlcNAc residues lacking Fuc (Rademacher et al., 2008). In contrast, recombinant human lactoferrin isolated from maize seeds was reported to contain pauci-Man-type N-glycans with β(1,2)-Xyl and α(1,3)-linked core Fuc (Samyn-Petit et al., 2001). Interestingly, this glycan pattern suggests a vacuolar location of this recombinant protein, and provides a second strong evidence for the presence of PSVs in maize, although the actual subcellular localization of lactoferrin in maize endosperm cells has not been confirmed.In previous studies we have shown that recombinant glycoproteins can help to clarify questions about the intracellular trafficking of proteins in cereal endosperm, and we found that a recombinant fungal phytase, although secreted from leaf cells, is mainly localized in the PSVs of wheat and rice endosperm (Arcalis et al., 2004; Drakakaki et al., 2006). In this study we used recombinant phytase to facilitate the visualization and characterization of the PSVs in maize, and we followed the intracellular fate of recombinant phytase in developing endosperm using a combination of microscopy and N-glycan analysis, revealing that the trafficking of the protein does indeed change as the seed matures. This behavior is mirrored by the two endogenous (aglycosylated) globulins, CAG and CL-1, indicating that the diversion of storage proteins may be a common strategy in seed development.     

Enrichment of homologs in insignificant BLAST hits by co-complex network alignment

Background  

Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stringent score cutoff is applied to distinguish putative homologs from possible false positive hits. As a consequence, some BLAST hits are discarded that are in fact homologous.