Plant peptides and peptidomics

Extracellular plant peptides perform a large variety of functions, including signalling and defence. Intracellular peptides often have physiological functions or may merely be the products of general proteolysis. Plant peptides have been identified and, in part, functionally characterized through biochemical and genetic studies, which are lengthy and in some cases impractical. Peptidomics is a branch of proteomics that has been developed over the last 5 years, and has been used mainly to study neuropeptides in animals and the degradome of proteases. Peptidomics is a fast, efficient methodology that can detect minute and transient amounts of peptides and identify their post-translational modifications. This review describes known plant peptides and introduces the use of peptidomics for the detection of novel plant peptides.     

Molecular dynamics simulation of the cooperative adsorption of barley lipid transfer protein and cis-isocohumulone at the vacuum-water interface

Molecular dynamic simulations have been carried out on systems containing a mixture of barley lipid transfer protein (LTP) and cis-isocohumulone (a hop derived iso-alpha-acid) in one of its enol forms, in bulk water and at the vacuum-water interface. In solution, the cis-isocohumulone molecules bind to the surface of the LTP molecule. The mechanism of binding appears to be purely hydrophobic in nature via desolvation of the protein surface. Binding of hop acids to the LTP leads to a small change in the 3-D conformation of the protein, but no change in the proportion of secondary structure present in helices, even though there is a significant degree of hop acid binding to the helical regions. At the vacuum-water interface, cis-isocohumulone shows a high surface activity and adsorbs rapidly at the interface. LTP then shows a preference to bind to the preadsorbed hop acid layer at the interface rather than to the bare water-vacuum interface. The free energy of adsorption of LTP at the hop-vacuum-water interface is more favorable than for adsorption at the vacuum-water interface. Our results support the view that hop iso-alpha-acids promote beer foam stability by forming bridges between separate adsorbed protein molecules, thus strengthening the adsorbed protein layer and reducing foam breakdown by lamellar phase drainage. The results also suggest a second mechanism may also occur, whereby the concentration of protein at the interface is increased via enhanced protein adsorption to adsorbed hop acid layers. This too would increase foam stability through its effect on the stabilizing protein layer around the foam bubbles.     

State of the art technologies to explore long non‐coding RNAs in cancer

Long non‐coding RNAs (lncRNAs) comprise a vast repertoire of RNAs playing a wide variety of crucial roles in tissue physiology in a cell‐specific manner. Despite being engaged in myriads of regulatory mechanisms, many lncRNAs have still remained to be assigned any functions. A constellation of experimental techniques including single‐molecule RNA in situ hybridization (sm‐RNA FISH), cross‐linking and immunoprecipitation (CLIP), RNA interference (RNAi), Clustered regularly interspaced short palindromic repeats (CRISPR) and so forth has been employed to shed light on lncRNA cellular localization, structure, interaction networks and functions. Here, we review these and other experimental approaches in common use for identification and characterization of lncRNAs, particularly those involved in different types of cancer, with focus on merits and demerits of each technique.     

Low temperature protocol for efficient transformation ofMycobacterium smegmatis spheroplasts

Spheroplasts ofMycobacterium smegmatis LM15, strain 607, were prepared by a combined treatment with glycine and lysozyme. The spheroplasts were tested for ability to take up and express purified mycobacteriophage DNA. Exposure of 1.0×10⁸ to 1.0×10⁹ spheroplasts to saturing DNA (1 g) for 15 min at 5°C resulted in a transfection efficiency of approximately 0.009%. The transfer of the -lactamase marker with DNA purified from strain LM15 to spheroplasts of a -lactamase-negative mutant, strain LM144, was achieved. The DNA-treated cultures, after reversion to the bacillary form, contained 20-fold more penicillinresistant cells than the nontreated control culture. Approximately 80% of the penicillin-resistant colonies from the DNA-treated cells were positive for -lactamase. Cell-free extracts of penicillin-resistant transformants contained -lactamase activity that ranged from 0.046 to 0.134 mol of benzylpencillin hydrolyzed/min per mg protein. This low temperature procedure is recommended for high efficiency transformation ofM. smegmatis.     

Biosynthesis and deposition of a noncovalent laminin-heparan sulfate proteoglycan complex and other basal lamina components by a human malignant cell line

The basal lamina components laminin, heparan sulfate proteoglycan (HSPG), and type IV collagen were synthesized and codeposited in the extracellular matrix (ECM) by a cultured human cell line from gestational choriocarcinoma (JAR). Laminin and HSPG formed a noncovalent complex detected by the coimmunoprecipitation of HSPG with laminin from cell lysates and culture media. The complex was stable in the cell lysis buffer that contained detergents (1% Triton X-100, 0.5% deoxycholate, and 0.1% sodium dodecyl sulfate) and sodium chloride (from 0.15 to 1.0 M), but was dissociated by adding 8 M urea to the detergent lysates. Even though JAR cells produced roughly equal amounts of HSPG and chondroitin sulfate proteoglycan, only HSPG complexed with laminin, suggesting a specific interaction between these basal lamina components. The laminin-HSPG complex was deposited and retained in the ECM. This was shown biochemically by isolating an enriched fraction of ECM from JAR cells cultured on native type I collagen gels. At steady state, more than half (52%) of the laminin-HSPG in the culture was recovered in the ECM fraction, in contrast to 16% of the total laminin and 29% of the total type IV collagen, which were secreted to a greater extent than laminin-HSPG into the culture medium. The retention of the laminin-HSPG complex in the ECM suggests that it may participate in the assembly of the basal lamina-like extracellular matrix deposited by JAR cultures. Omission of ascorbate from the culture medium abolished the ECM deposition of type IV collagen but had little effect on the deposition of laminin or laminin-HSPG. This demonstrates that the stable deposition of laminin-HSPG and laminin in the collagen-based choriocarcinoma cultures is not dependent on an assembled network of type IV collagen.     

Genomic sequence and receptor for the Vibrio cholerae phage KSF-1phi: evolutionary divergence among filamentous vibriophages mediating lateral gene transfer

KSF-1phi, a novel filamentous phage of Vibrio cholerae, supports morphogenesis of the RS1 satellite phage by heterologous DNA packaging and facilitates horizontal gene transfer. We analyzed the genomic sequence, morphology, and receptor for KSF-1phi infection, as well as its phylogenetic relationships with other filamentous vibriophages. While strains carrying the mshA gene encoding mannose-sensitive hemagglutinin (MSHA) type IV pilus were susceptible to KSF-1phi infection, naturally occurring MSHA-negative strains and an mshA deletion mutant were resistant. Furthermore, d-mannose as well as a monoclonal antibody against MSHA inhibited infection of MSHA-positive strains by the phage, suggesting that MSHA is the receptor for KSF-1phi. The phage genome comprises 7,107 nucleotides, containing 14 open reading frames, 4 of which have predicted protein products homologous to those of other filamentous phages. Although the overall genetic organization of filamentous phages appears to be preserved in KSF-1phi, the genomic sequence of the phage does not have a high level of identity with that of other filamentous phages and reveals a highly mosaic structure. Separate phylogenetic analysis of genomic sequences encoding putative replication proteins, receptor-binding proteins, and Zot-like proteins of 10 different filamentous vibriophages showed different results, suggesting that the evolution of these phages involved extensive horizontal exchange of genetic material. Filamentous phages which use type IV pili as receptors were found to belong to different branches. While one of these branches is represented by CTXphi, which uses the toxin-coregulated pilus as its receptor, at least four evolutionarily diverged phages share a common receptor MSHA, and most of these phages mediate horizontal gene transfer. Since MSHA is present in a wide variety of V. cholerae strains and is presumed to express in the environment, diverse filamentous phages using this receptor are likely to contribute significantly to V. cholerae evolution.     

Simultaneous quantification of emtricitabine and tenofovir in human plasma using high-performance liquid chromatography after solid phase extraction

An accurate, sensitive and simple reverse-phase (RP) high-performance liquid chromatography (HPLC) assay for the simultaneous quantitative determination of emtricitabine and tenofovir in human blood plasma is described. Using 200 microL of plasma and BOND ELUT-C18 Varian columns, the solid phase extraction (SPE) method results in a clean baseline and high extraction efficiencies (100% for emtricitabine and 98.6% for tenofovir). An Atlantistrade mark dC-18 analytical column is used along with an 18 min linear gradient elution of phosphate buffer (pH 5.7) and methanol to provide sharp peaks for emtricitabine at 280 nm, tenofovir at 259 nm, and the internal standard 2',3'didoxyuridine (DDU) at 262 nm. The method was validated over the range of 10-10,000 ng/mL for both analytes, and is accurate (average accuracies of three different concentrations ranged from 98 to 105% for emtricitabine and 97 to 103% for tenofovir) and precise (within- and between-day precision ranged from 1.7 to 3.7% and 3.7 to 5.2%, respectively). This method is suitable for use in clinical pharmacokinetic studies and is nimble enough for therapeutic drug monitoring.     

Endophytic bacterium Bacillus subtilis (BERA 71) improves salt tolerance in chickpea plants by regulating the plant defense mechanisms

Plant growth-promoting endophytic bacteria can stimulate the growth, nutrient acquisition, symbiotic performance and stress tolerance of chickpea plants under saline soil conditions. The aim of this study was to investigate the stress-adaptive mechanisms of chickpea plants mediated by Bacillus subtilis (BERA 71) under saline conditions. Inoculation with BERA 71 enhanced plant biomass and the synthesis of photosynthetic pigments and reduced the levels of reactive oxygen species (ROS) and lipid peroxidation in plants under conditions of stress. Furthermore, the activities of ROS-scavenging antioxidant enzymes (superoxide dismutase, peroxidase, catalase and glutathione reductase), the levels of non-enzymatic antioxidants (ascorbic acid and glutathione) and the total phenol content were increased in stressed plants during bacterial association. The bacteria decreased sodium accumulation and enhanced the nitrogen, potassium, calcium and magnesium content in the plants. The suppression of ROS generation and of lipid peroxidation and the accumulation of proline in BERA-71-inoculated plants enhanced the membrane stability under salinity stress and non-stress conditions.