Rapid classification of phenotypic mutants of Arabidopsis via metabolite fingerprinting

We evaluated the application of gas chromatography-mass spectrometry metabolic fingerprinting to classify forward genetic mutants with similar phenotypes. Mutations affecting distinct metabolic or signaling pathways can result in common phenotypic traits that are used to identify mutants in genetic screens. Measurement of a broad range of metabolites provides information about the underlying processes affected in such mutants. Metabolite profiles of Arabidopsis (Arabidopsis thaliana) mutants defective in starch metabolism and uncharacterized mutants displaying a starch-excess phenotype were compared. Each genotype displayed a unique fingerprint. Statistical methods grouped the mutants robustly into distinct classes. Determining the genes mutated in three uncharacterized mutants confirmed that those clustering with known mutants were genuinely defective in starch metabolism. A mutant that clustered away from the known mutants was defective in the circadian clock and had a pleiotropic starch-excess phenotype. These results indicate that metabolic fingerprinting is a powerful tool that can rapidly classify forward genetic mutants and streamline the process of gene discovery.     

Polygalacturonase-inhibiting protein is a structural component of plant cell wall

It is generally believed that plants "evolved a strategy of defending themselves from a phytopathogen attack" during evolution. This metaphor is used frequently, but it does not facilitate understanding of the mechanisms providing plant resistance to the invasion of foreign organisms and to other unfavorable external factors, as well as the role of these mechanisms in plant growth and development. Information on processes involving one of the plant resistance factors--polygalacturonase-inhibiting protein (PGIP)--is considered in this review. The data presented here indicate that PGIP, being an extracellular leucine-rich repeat-containing protein, performs important functions in the structure of plant cell wall. Amino acid residues participating in PGIP binding to homogalacturonan in the cell wall have been determined. The degree of methylation and the mode of distribution of homogalacturonan methyl groups are responsible for the formation of a complex structure, which perhaps determines the specificity of PGIP binding to pectin. PGIP is apparently one of the components of plant cell wall determining some of its mechanical properties; it is involved in biochemical processes related to growth, expansion, and maceration, and it influences plant morphology. Polygalacturonase (PG) is present within practically all plant tissues, but the manifestation of its activity varies significantly depending on physiological conditions in the tissue. Apparently, the regulation of PG functioning in apoplast significantly affects the development of processes associated with the modification of the structure of plant cell wall. PGIP can regulate PG activity through binding to homogalacturonan. The genetically determined structure of PGIP in plants determines the mode of its interaction with an invader and perhaps is one of the factors responsible for the set of pathogens causing diseases in a given plant species.     

Mechanical modeling and structural analysis of the primary plant cell wall

Plant cell growth is a fundamental process during plant development whose spatial and temporal dynamics are controlled by the cell wall. Modeling mechanical aspects of cell growth therefore requires the integration of structural cell wall details with quantitative biophysical parameters. Recent advances in microscopic techniques and mechanical modeling have made significant contributions to the field of cell wall biomechanics. Live observation of cellulose microfibrils at high z-resolution now enables determining the dynamic orientation of these polymers in the different wall layers of growing cells. Mechanical modeling approaches have been developed to operate at the scale of individual molecules and will thus be able to exploit the availability of the high-resolution structural data. The combination of these techniques has the potential to make a significant and quantitative contribution to our understanding of plant growth and development.     

Rapid deposition of wheat cell wall structural proteins in response to Fusarium-derived elicitors

Two novel cell wall structural proteins of spring wheat (Triticum aestivum L. em Thell.). undergo rapid deposition in the cell wall matrix in a H(2)O(2)-dependent reaction after the elicitation of cultures with Fusarium graminearum (L.)-derived elicitor. The amino acid compositions of these proteins were remarkably similar and indicated that they were highly acidic (pI 3.8). These proteins contained 13--17% each of Gly, Glx and Ser with lesser amounts (6--8%) of Ala, Asx and Thr, and it has been suggested that they are known as glycine- and serine-rich proteins (GSRPs). SELDI-MS ionization spectra demonstrated that these proteins have low molecular masses of 8590 and 4292 Da. These results are discussed in relation to the possible role of these novel proteins in rapid, cell wall defensive reactions to pathogenic attack.     

The plant cell wall

<正>Research on the many aspects of the plant cell wall has experienced rejuvenation during the past few years.This is perhaps mainly due to the commercial interest in the chemical components of the cell wall that have potential for industrial use:Cellulose for fi bers and together with hemicelluloses for bioethanol,lignin for plastics or biofuel,pectins as gel agents,let alone woody cell wall material for construction or pulp     

Rapid identification of proteins by peptide-mass fingerprinting

BACKGROUND: Developments in 'soft' ionisation techniques have revolutionized mass-spectro-metric approaches for the analysis of protein structure. For more than a decade, such techniques have been used, in conjuction with digestion b specific proteases, to produce accurate peptide molecular weight 'fingerprints' of proteins. These fingerprints have commonly been used to screen known proteins, in order to detect errors of translation, to characterize post-translational modifications and to assign diulphide bonds. However, the extent to which peptide-mass information can be used alone to identify unknown sample proteins, independent of other analytical methods such as protein sequence analysis, has remained largely unexplored. RESULTS: We report here on the development of the molecular weight search (MOWSE) peptide-mass database at the SERC Daresbury Laboratory. Practical experience has shown that sample proteins can be uniquely identified from a few as three or four experimentally determined peptide masses when these are screened against a fragment database that is derived from over 50 000 proteins. Experimental errors of a few Daltons are tolerated by the scoring algorithms, thus permitting the use of inexpensive time-of-flight mass spectrometers. As with other types of physical data, such as amino-acid composition or linear sequence, peptide masses provide a set of determinants that are sufficiently discriminating to identify or match unknown sample proteins. CONCLUSION: Peptide-mass fingerprints can prove as discriminating as linear peptide sequences, but can be obtained in a fraction of the time using less protein. In many cases, this allows for a rapid identification of a sample protein before committing it to protein sequence analysis. Fragment masses also provide information, at the protein level, that is complementary to the information provided by large-scale DNA sequencing or mapping projects.     

Rapid apolipoprotein E phenotyping by immunofixation in agarose

Conventional determination of apolipoprotein E isomorphs comprises ultracentrifugation of 1-5 ml serum, delipidation of very low density lipoproteins (VLDL), and isoelectric focusing (IEF) in polyacrylamide gels. In order to reduce the sample volume and to avoid nonspecific protein bands, immunoblotting was proposed. Now we describe a methodological variant that uses 25 microliters serum, replaces ultracentrifugation by precipitation of apoE-containing lipoproteins with polyethylene glycol, and delipidation by dissolution in detergent. IEF is carried out in agarose. This allows specific immunofixation of apoE-containing bands with 10 microliters antiserum per sample. This method yields apoE patterns that are specific and well resolved. Also, it offers considerable savings of time and equipment involved.     

酶解破壁促进废次烟叶中茄尼醇溶浸

协同应用纤维素酶和木质素酶催化降解废次烟叶,探讨清洁高效的酶解破壁效应及浸提茄尼醇工艺条件。结果发现复配酶催化裂解溶浸茄尼醇效果明显优于单一酶,酶解时间、温度、pH值以及酶投加量等条件均影响酶破壁浸提茄尼醇能效。结果表明,采用纤维素酶：木质素酶酶活比15∶1 (U/U) 的复配酶,在体积为5倍烟草质量的水介质环境中,当复配酶投加量为175 U/g,水浴温度40 ℃,pH=6时,催化酶解烟叶8 h后,茄尼醇溶浸浓度可达0.33 g/L。在此条件下,茄尼醇平均提取率可达96.53％,是化学回流浸提方法的1.68倍。该方法为有效提取废次烟草中茄尼醇提供了一种新途径。     

Growth of the plant cell wall

Plant cells encase themselves within a complex polysaccharide wall, which constitutes the raw material that is used to manufacture textiles, paper, lumber, films, thickeners and other products. The plant cell wall is also the primary source of cellulose, the most abundant and useful biopolymer on the Earth. The cell wall not only strengthens the plant body, but also has key roles in plant growth, cell differentiation, intercellular communication, water movement and defence. Recent discoveries have uncovered how plant cells synthesize wall polysaccharides, assemble them into a strong fibrous network and regulate wall expansion during cell growth.     

Rapid DNA fingerprinting of pathogens by flow cytometry

BACKGROUND: A new method for rapid discrimination among bacterial strains based on DNA fragment sizing by flow cytometry is presented. This revolutionary approach combines the reproducibility and reliability of restriction fragment length polymorphism (RFLP) analysis with the speed and sensitivity of flow cytometry. METHODS: Bacterial genomic DNA was isolated and digested with a rare-cutting restriction endonuclease. The resulting fragments were stained stoichiometrically with PicoGreen dye and introduced into an ultrasensitive flow cytometer. A histogram of burst sizes from the restriction fragments (linearly related to fragment length in base pairs) resulted in a DNA fingerprint that was used to distinguish among different bacterial strains. RESULTS: Five different strains of gram-negative Escherichia coli and six different strains of gram-positive Staphylococcus aureus were distinguished by analyzing their restriction fragments with DNA fragment sizing by flow cytometry. Fragment distribution analyses of extracted DNA were approximately 100 times faster and approximately 200,000 times more sensitive than pulsed-field gel electrophoresis (PFGE). When sample preparation time is included, the total DNA fragment analysis time was approximately 8 h by flow cytometry and approximately 24 h by PFGE. CONCLUSIONS: DNA fragment sizing by flow cytometry is a fast and reliable technique that can be applied to the discrimination among species and strains of human pathogens. Unlike some polymerase chain reaction (PCR)-based methods, sequence information about the bacterial strains is not required, allowing the detection of unknown, newly emerged, or unanticipated strains.     

Specific type of secondary cell wall formed by plant fibers

The review sums data indicating that, in many plant fibers, the secondary cell wall contains so-called gelatinous layers of peculiar structure along with those of common (xylan) structure. Sometimes these gelatinous layers comprise the main bulk of the cell wall. Key characteristics of gelatinous cell wall are presented and compared with those of classic xylan-type cell wall. The process of gelatinous cell wall formation is considered in detail for flax phloem fibers; several characteristic features of this process were revealed: intense rearrangement of already deposited cell-wall layers, unusual dynamics of Golgi vesicles, the occurrence of the stage-specific polysaccharide with specific properties, high activity of β-galactosidase, and the presence of substantial amount of free galactose. Similarity and differences in the gelatinous cell wall formation in the fibers of various plant species are discussed.     

Elevated cell wall serine in pleiotropic staphylococcal mutants

Korman, Ruth Z. (Cornell University, Ithaca, N.Y.). Elevated cell wall serine in pleiotropic staphylococcal mutants. J. Bacteriol. 92:762-768. 1966.-Physically purified cell walls were prepared from two staphylococcal strains and from pleiotropic variants derived from them. The quantitative amino acid and amino sugar content of these walls is reported. The pleiotypes, which are identified culturally by their failure to elaborate coagulase, their resistance to bacteriophage, and their sensitivity to mannitol, have altered molar ratios of amino acids and amino sugars in their cell walls. In comparison with lysine content, the serine content of the mutant wall is elevated and the glycine content is reduced. The glucosamine content is reduced also. It is postulated that the pleiotropic mutants possess an altered cell wall biosynthetic pathway.     

Saccharomyces cerevisiae structural cell wall mannoprotein

A novel mannoprotein fraction with an average molecular weight of 180 000 has been isolated from Saccharomyces cerevisiae mnn9 mutant cell wall that was solubilized by beta-glucanase digestion. The same material could be extracted from purified wall fragments with 1% sodium dodecyl sulfate. The protein component, 12% by weight, is rich in proline, whereas the carbohydrate, mainly mannose, is about evenly distributed between asparagine and hydroxyamino acids. Endoglucosaminidase H digestion of the isolated mannoprotein reduced its average molecular weight to 150 000, but the mannoprotein, while still embedded in the cell wall, was inaccessible to the enzyme. Biosynthesis and translocation of the mannoprotein were investigated by following incorporation of [3H]proline into this fraction. In the presence of tunicamycin, both mnn9 and wild-type X2180 cells made a mannoprotein fraction with an average molecular weight of 140 000, whereas in the absence of the glycosylation inhibitor, the mnn9 mutant made material with a molecular weight of 180 000 and the mannoprotein made by wild-type cells was too large to penetrate the polyacrylamide gel. Although the cell wall mannoprotein was resistant to heat and proteolytic enzymes, attempts to isolate the carbohydrate-free component failed to yield any characteristic peptide material.