Annuals sprouting adventitiously from the hypocotyl: their compensatory growth and implications for weed management

Habitats, disturbed severely at least once a year, are often dominated by annual plants, which avoid disturbance by means of a short life span and massive production of seeds. Contrary to perennials, they lack pools of reserve meristems on and storage carbon in below-ground organs necessary for vegetative regeneration after disturbance. However, some annuals are able to initiate a bud bank on the hypocotyl after loss of their shoot. In three experiments, we investigated how the timing of disturbance or population origin affects adventitious bud formation on the hypocotyl for regeneration and compensatory growth in some annual weeds.     

Effects of the Mi-1 and the N root-knot nematode-resistance gene on infection and reproduction of Meloidogyne enterolobii on tomato and pepper cultivars

Meloidogyne enterolobii is widely considered to be an aggressive root-knot nematode species that is able to reproduce on root-knot nematode-resistant tomato and pepper cultivars. In greenhouse experiments, M. enterolobii isolates 1 and 2 from Switzerland were able to reproduce on tomato cultivars carrying the Mi-1 resistance gene as well as an N-carrying pepper cultivar. Reproduction factors (Rf) ranged between 12 and 109 depending on the plant cultivar, with M. enterolobii isolate 2 being more virulent when compared to isolate 1. In contrast, M. arenaria completely failed to reproduce on these resistant tomato and pepper cultivars. Although some variability in virulence and effectiveness of root-knot nematode-resistance genes was detected, none of the plant cultivars showed Rf values less than 1 or less than 10% of the reproduction observed on the susceptible cv. 'Moneymaker' (Rf = 23-44) used to characterize resistance. The ability of M. enterolobii to overcome the resistance of tomato and pepper carrying the Mi-1 and the N gene makes it difficult to manage this root-knot nematode species, particularly in organic farming systems where chemical control is not an option.     

The Lipidomes of Vesicular Stomatitis Virus,Semliki Forest Virus,and the Host Plasma Membrane Analyzed by Quantitative Shotgun Mass Spectrometry

Although enveloped virus assembly in the host cell is a crucial step in the virus life cycle, it remains poorly understood. One issue is how viruses include lipids in their membranes during budding from infected host cells. To analyze this issue, we took advantage of the fact that baby hamster kidney cells can be infected by two different viruses, namely, vesicular stomatitis virus and Semliki Forest virus, from the Rhabdoviridae and Togaviridae families, respectively. We purified the host plasma membrane and the two different viruses after exit from the host cells and analyzed the lipid compositions of the membranes by quantitative shotgun mass spectrometry. We observed that the lipid compositions of these otherwise structurally different viruses are virtually indistinguishable, and only slight differences were detected between the viral lipid composition and that of the plasma membrane. Taken together, the facts that the lipid compositions of the two viruses are so similar and that they strongly resemble the composition of the plasma membrane suggest that these viruses exert little selection in including lipids in their envelopes.Enveloped viruses acquire their lipid envelope from the membranes of host cells (43). In this process, the nucleocapsid or the nucleocapsid-matrix complex of the viruses buds out of the cell and becomes enveloped by a segment of the host membrane. This membrane segment is modified during the budding process, such that virally encoded membrane proteins are included in the viral envelope, while most host proteins are excluded. Since viruses usually do not carry lipid-synthesizing enzymes, the lipids in the viral envelope are derived from the host membrane. The lipid compositions of enveloped viruses have been studied for years (2, 15, 17, 18, 23, 25, 34, 36, 38, 40). One question that remains to be answered is whether the lipids are included passively, and thus the lipid composition of the envelope reflects the lipid composition of the host membrane, or whether lipid sorting occurs, leading to selective inclusion of some lipids and exclusion of others. This issue has been complicated by the fact that the lipid bilayer is no longer considered a homogenous liquid but contains fluctuating nanoscale assemblies of sphingolipids, saturated phospholipids, cholesterol (Chol), and proteins, called lipid rafts (13, 44). Lipid rafts can be induced to coalesce—usually by protein-protein interactions—into larger, dynamic platforms that function in signal transduction, intracellular membrane transport, and other membrane functions (45). It was also proposed that viruses make use of these membrane domains during their exit from cells (29, 32).A major complication in comparing viral envelopes with host cell membranes is the difficulty in obtaining host cell membranes of purity similar to that of the easily purified viruses. Many studies are faulted by the impurity of the cell membranes analyzed. Moreover, the early work in this field employed conventional analytical methods (such as thin-layer chromatography) that provide only semiquantitative estimates of the total abundance of the major lipid classes. Most importantly, lipid species diversity could not be analyzed. Recent developments in mass spectrometry (MS) have enabled comprehensive and quantitative analyses of lipidomes at the level of individual molecular species. The lipidomes of human immunodeficiency virus (HIV), murine leukemia virus (6, 7), and several bacteriophages (20, 21) were recently analyzed by these new methods.This paper focuses on two well-characterized enveloped viruses, Semliki Forest virus (SFV) and vesicular stomatitis virus (VSV). SFV is an RNA virus belonging to the Togaviridae family of the Alphaviridae that acquires its envelope by budding from the host cell plasma membrane (PM) (46). Early studies analyzed the lipid composition of the viral envelope and also that of the host cell PM (39, 40). These studies revealed strong similarity between the envelope of SFV and the host PM, but one important discrepancy was the higher Chol-to-phospholipid ratio in the virus.VSV is an RNA virus belonging to the Rhabdoviridae family and also hijacks its envelope from the host cell PM (35), but the lipid specificity of the budding process remains controversial. The most recent studies claim that VSV buds from localized regions that do not reflect the average composition of the PM (23, 36). It has also been claimed that lipid rafts are involved in VSV envelope assembly during budding (37).We used BHK-21 cells as host cells to purify SFV and VSV. The purposes of this study were (i) to establish a robust, comprehensive, and quantitative method to analyze lipidomes, including the full complement of glycerolipid, glycerophospholipid, and sphingolipid species as well as Chol; (ii) to establish a protocol for purification of PM suitable for MS analysis; and (iii) to analyze and compare the lipidomes of SFV, VSV, and the BHK-21 PM.We found that the lipidomes of SFV and VSV are similar in molecular composition and are closely related to that of the BHK-21 PM. The small differences observed could be explained by the high degrees of curvature generated during the viral budding process.     

Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation

Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.Enzymatic reduction of U(VI) to insoluble U(IV) by dissimilatory Fe(III)-reducing bacteria (DIRB) can limit subsurface U(VI) migration (2, 19, 20). This observation provided the basis for an important new biotechnology that involves remediation of contaminated groundwater by organic amendment-based stimulation of the activities of DIRB. Despite the obvious high potential value, there are significant technological challenges that must be overcome before this approach can be deployed as a functional biotechnology. In situ U(VI) reduction rates are directly coupled with microbial physiology and community composition, both of which change as bioremediation progresses (22, 24, 28). Thus, a key need is the ability to monitor changes in microbial community membership and function as they occur, so that optimal management strategies can be implemented to achieve the desired geochemical outcomes. This challenge is significant because metal reduction occurs within pore spaces deep in the aquifer and the process is associated with vast numbers of microbial cells distributed in the subsurface.Changes in the complements of DIRB proteins should reflect shifts in microbial physiology and could be used to monitor in situ bioremediation technologies if microbial proteomes could be tracked during organic amendment. Proteomic methods have previously been used to detect physiological responses of microorganisms growing in pure culture (8, 16, 17) and in genomically characterized natural microbial communities (7, 18, 26, 34). Strain-resolved proteomic approaches (18) have the potential to also track changes in microbial community composition. Previously, the use of proteomic analysis techniques to monitor subsurface bioremediation has been precluded by the lack of metagenomic data. Here, we used seven isolate Geobacter genomes to generate a reference database against which peptide data measured using two-dimensional (2D) liquid chromatography (LC)-based high-resolution tandem mass spectrometry (MS-MS) were compared for protein identification. Although differences between environmental and isolate peptide sequences may preclude peptide identification, peptides common to multiple Geobacter types and isolates enable protein identification, and peptides unique to one isolate constrain environmental genotypes. Simultaneous analysis of community structure and function in natural microbial communities that relies upon proteomics-derived genomic insights is referred to as proteogenomics (Fig. ​(Fig.1).1). In the current study, a proteogenomic approach was applied to monitor the progress of an in situ U bioremediation project carried out at the Department of Energy (DOE) Integrated Field Research Challenge site in Rifle, CO. Despite strain complexity in the recovered samples, proteomic data provided insights into the community structure and physiology of planktonic Geobacter isolates in aquifer solutions as groundwater U(VI) concentrations decreased.Open in a separate windowFIG. 1.Strain-resolved proteogenomic techniques allow identification of unique peptides and constrain the genotypes present in environmental samples. (1) Proteins were predicted from the seven isolate Geobacter genomes. (2) Proteins were aligned. In the example shown, they share a conserved region (similar colors in all seven regions) and have a variable region (indicated by the variety of colors for each protein). (3) Tryptic digest patterns are used to predict peptide sequences. Proteins were extracted from the experimental sample (4) and digested into peptides by using trypsin (5). These peptides were separated using LC (6) before high-resolution mass spectrometry on a fraction of peptides from an elution peak (7) to determine the mass of the parent ions. (8) The peptides are fragmented and mass spectrometry measurements made on fragment ions. (9) Mass spectral data are matched to peptide sequences predicted in step 3 to allow peptide identification. Peptide sequences differing by only one amino acid can be identified, as shown in the spectral diagram. (10) Detected peptides are mapped onto aligned protein sequences to identify peptides shared or unique to each of the isolate species. Spectral counts can be mapped together with peptides. Where coexisting unique peptides are detected, ratios of unique spectral counts can be used to infer relative strain abundance. As shown, the identification of a unique peptide indicates that this protein is most closely related to that of G. bemidjiensis.     

Use of 4-sulfophenyl isothiocyanate labeling and mass spectrometry to determine the site of action of the streptococcolytic peptidoglycan hydrolase zoocin A

Zoocin A is a streptococcolytic peptidoglycan hydrolase with an unknown site of action that is produced by Streptococcus equi subsp. zooepidemicus 4881. Zoocin A has now been determined to be a d-alanyl-l-alanine endopeptidase by digesting susceptible peptidoglycan with a combination of mutanolysin and zoocin A, separating the resulting muropeptides by reverse-phase high-pressure liquid chromatography, and analyzing them by mass spectrometry (MS) in both the positive- and negative-ion modes to determine their compositions. In order to distinguish among possible structures for these muropeptides, they were N-terminally labeled with 4-sulfophenyl isothiocyanate (SPITC) and analyzed by tandem MS in the negative-ion mode. This novel application of SPITC labeling and MS/MS analysis can be used to analyze the structure of peptidoglycans and to determine the sites of action of other peptidoglycan hydrolases.     

β‐arrestin1 phosphorylation by GRK5 regulates G protein‐independent 5‐HT4 receptor signalling

G protein‐coupled receptors (GPCRs) have been found to trigger G protein‐independent signalling. However, the regulation of G protein‐independent pathways, especially their desensitization, is poorly characterized. Here, we show that the G protein‐independent 5‐HT₄ receptor (5‐HT₄R)‐operated Src/ERK (extracellular signal‐regulated kinase) pathway, but not the G_s pathway, is inhibited by GPCR kinase 5 (GRK5), physically associated with the proximal region of receptor’ C‐terminus in both human embryonic kidney (HEK)‐293 cells and colliculi neurons. This inhibition required two sequences of events: the association of β–arrestin1 to a phosphorylated serine/threonine cluster located within the receptor C‐t domain and the phosphorylation, by GRK5, of β–arrestin1 (at Ser⁴¹²) bound to the receptor. Phosphorylated β‐arrestin1 in turn prevented activation of Src constitutively bound to 5‐HT₄Rs, a necessary step in receptor‐stimulated ERK signalling. This is the first demonstration that β‐arrestin1 phosphorylation by GRK5 regulates G protein‐independent signalling.     

High-throughput SPR sensor for food safety

High-throughput surface plasmon resonance (SPR) biosensor for rapid and parallelized detection of nucleic acids identifying specific bacterial pathogens is reported. The biosensor consists of a high-performance SPR imaging sensor with polarization contrast and internal referencing (refractive index resolution 2 x 10(-7) RIU) and an array of DNA probes microspotted on the surface of the SPR sensor. It is demonstrated that short sequences of nucleic acids (20-23 bases) characteristic for bacterial pathogens such as Brucella abortus, Escherichia coli, and Staphylococcus aureus can be detected at 100 pM levels. Detection of specific DNA or RNA sequences can be performed in less than 15 min by the reported SPR sensor.     

Characterization of protein glycosylation in Francisella tularensis subsp. holarctica: identification of a novel glycosylated lipoprotein required for virulence

FTH_0069 is a previously uncharacterized strongly immunoreactive protein that has been proposed to be a novel virulence factor in Francisella tularensis. Here, the glycan structure modifying two C-terminal peptides of FTH_0069 was identified utilizing high resolution, high mass accuracy mass spectrometry, combined with in-source CID tandem MS experiments. The glycan observed at m/z 1156 was determined to be a hexasaccharide, consisting of two hexoses, three N-acetylhexosamines, and an unknown monosaccharide containing a phosphate group. The monosaccharide sequence of the glycan is tentatively proposed as X-P-HexNAc-HexNAc-Hex-Hex-HexNAc, where X denotes the unknown monosaccharide. The glycan is identical to that of DsbA glycoprotein, as well as to one of the multiple glycan structures modifying the type IV pilin PilA, suggesting a common biosynthetic pathway for the protein modification. Here, we demonstrate that the glycosylation of FTH_0069, DsbA, and PilA was affected in an isogenic mutant with a disrupted wbtDEF gene cluster encoding O-antigen synthesis and in a mutant with a deleted pglA gene encoding pilin oligosaccharyltransferase PglA. Based on our findings, we propose that PglA is involved in both pilin and general F. tularensis protein glycosylation, and we further suggest an inter-relationship between the O-antigen and the glycan synthesis in the early steps in their biosynthetic pathways.     

The Arabidopsis HEI10 Is a New ZMM Protein Related to Zip3

In numerous species, the formation of meiotic crossovers is largely under the control of a group of proteins known as ZMM. Here, we identified a new ZMM protein, HEI10, a RING finger-containing protein that is well conserved among species. We show that HEI10 is structurally and functionally related to the yeast Zip3 ZMM and that it is absolutely required for class I crossover (CO) formation in Arabidopsis thaliana. Furthermore, we show that it is present as numerous foci on the chromosome axes and the synaptonemal complex central element until pachytene. Then, from pachytene to diakinesis, HEI10 is retained at a limited number of sites that correspond to class I COs, where it co-localises with MLH1. Assuming that HEI10 early staining represents an early selection of recombination intermediates to be channelled into the ZMM pathway, HEI10 would therefore draw a continuity between early chosen recombination intermediates and final class I COs.     

Ligand binding study of human PEBP1/RKIP: interaction with nucleotides and Raf-1 peptides evidenced by NMR and mass spectrometry

Background

Human Phosphatidylethanolamine binding protein 1 (hPEBP1) also known as Raf kinase inhibitory protein (RKIP), affects various cellular processes, and is implicated in metastasis formation and Alzheimer''s disease. Human PEBP1 has also been shown to inhibit the Raf/MEK/ERK pathway. Numerous reports concern various mammalian PEBP1 binding ligands. However, since PEBP1 proteins from many different species were investigated, drawing general conclusions regarding human PEBP1 binding properties is rather difficult. Moreover, the binding site of Raf-1 on hPEBP1 is still unknown.

Methods/Findings

In the present study, we investigated human PEBP1 by NMR to determine the binding site of four different ligands: GTP, FMN, and one Raf-1 peptide in tri-phosphorylated and non-phosphorylated forms. The study was carried out by NMR in near physiological conditions, allowing for the identification of the binding site and the determination of the affinity constants K_D for different ligands. Native mass spectrometry was used as an alternative method for measuring K_D values.

Conclusions/Significance

Our study demonstrates and/or confirms the binding of hPEBP1 to the four studied ligands. All of them bind to the same region centered on the conserved ligand-binding pocket of hPEBP1. Although the affinities for GTP and FMN decrease as pH, salt concentration and temperature increase from pH 6.5/NaCl 0 mM/20°C to pH 7.5/NaCl 100 mM/30°C, both ligands clearly do bind under conditions similar to what is found in cells regarding pH, salt concentration and temperature. In addition, our work confirms that residues in the vicinity of the pocket rather than those within the pocket seem to be required for interaction with Raf-1.