Functional rescue of a bacterial dapA auxotroph with a plant cDNA library selects for mutant clones encoding a feedback-insensitive dihydrodipicolinate synthase

Dihydrodipicolinate synthase (DHDPS; EC4.2.1.52) catalyses the first reaction of lysine biosynthesis in plants and bacteria. Plant DHDPS enzymes are strongly inhibited by lysine (I0.5 approximately 10 microM), whereas the bacterial enzymes are less (50-fold) or insensitive to lysine inhibition. We found that plant dhdps sequences expressing lysine-sensitive DHDPS enzymes are unable to complement a bacterial auxotroph, although a functional plant DHDPS enzyme is formed. As a consequence of this, plant dhdps cDNA clones which have been isolated through functional complementation using the DHDPS-deficient Escherichia coli strain encode mutated DHDPS enzymes impaired in lysine inhibition. The experiments outlined in this article emphasize that heterologous complementation can select for mutant clones when altered protein properties are requisite for functional rescue. In addition, the mutants rescued by heterologous complementation revealed a new critical amino acid substitution which renders lysine insensitivity to the plant DHDPS enzyme. An interpretation is given for the impaired inhibition mechanism of the mutant DHDPS enzyme by integrating the identified amino acid substitution in the DHDPS protein structure.     

A numerical taxonomic study of the Pseudomonas flora isolated from poultry meat

Pseudomonas strains were isolated from both fresh and cold-stored broiler skin. Phenotypically-based numerical taxonomic techniques were used to characterize the isolates and 36 reference strains. For this purpose, Biolog GN Microplates, API 20NE and a number of other biochemical tests were used. Jaccard clustering revealed the predominance of four major Pseudomonas groups: Ps. fragi, Ps. lundensis, strains belonging to Ps. fluorescens biovars and an unidentified group of strains displaying a high degree of similarity to Ps. fluorescens biovars. Within Ps. fluorescens, biovar A was best represented. The marked proteolytic character of members of Ps. fluorescens biovars A, B and C, as well as of members of the unidentified cluster, supports their possible role in the origin of organoleptic defects. In the Ps. lundensis cluster, a distinct group of Ps. lundensis-like species was found. Further genotypic studies should be carried out to clarify the taxonomic status of the Ps. lundensis-like strains and that of the unidentified group resembling Ps. fluorescens biovars A and B.     

Construction and characterisation of a yeast artificial chromosome library containing five haploid sugarbeet (Beta vulgaris L.) genome equivalents

A yeast artificial chromosome (YAC) genomic library of Beta vulgaris was constructed in the pYAC4 vector. High-molecular-weight DNA was prepared from agarose-embedded leaf protoplasts from a triploid cultivar. The library was found to contain 33,500 clones in an ordered array of microtiter plates. Mean size of the inserts was estimated to be 135 kb, and the library should therefore represent the equivalent of five haploid genomes. The library was characterised for the presence of highly repetitive, chloroplast and single-copy sequences. In order to isolate single-copy sequences, 18 pools of DNA, each from 1920 individual YAC clones, were prepared for rapid screening of the library by the polymerase chain reaction. The results of these screenings showed that the number of isolated clones was at or near the frequency expected.     

Are classification and phytopathological diversity compatible in Xanthomonas?

The genus Xanthomonas is characterized by its phytopathogenic diversity and the host specificity of its members. In the past, the classification of the members of this genus has been based primarily on the criterion of host specificity. This has led to a classification system which focused only on naming phytopathogenic variants on different hosts. Extensive taxonomic examination of Xanthomonas has shown that the phytopathogenic specialization of the bacteria is not correlated with the actual relationships within the genus. Based upon total genomic DNA homology, the genus has been reclassified into 20 species. At present, non-pathogenic xanthomonads are frequently isolated from plant material. As these strains often cannot be classified to existing species, it becomes clear that the diversity of the genus is much greater than expected from the phytopathogenic subpopulation, which has been the primary subject in the past. The example of Xanthomonas also illustrates that attempts to divide bacterial populations into discrete taxa conflict with the actual continuous nature of biodiversity. Received 16 April 1996/ Accepted in revised form 27 September 1996     

Paratope determination of the antithrombotic antibody 82D6A3 based on the crystal structure of its complex with the von Willebrand factor A3-domain

The antithrombotic monoclonal antibody 82D6A3 is directed against amino acids Arg-963, Pro-981, Asp-1009, Arg-1016, Ser-1020, Met-1022, and His-1023 of the von Willebrand factor A3-domain (Vanhoorelbeke, K., Depraetere, H., Romijn, R. A., Huizinga, E., De Maeyer, M., and Deckmyn, H. (2003) J. Biol. Chem. 278, 37815-37821). By this, it potently inhibits the interaction of von Willebrand factor to collagens, which is a prerequisite for blood platelet adhesion to the injured vessel wall at sites of high shear. To fully understand the mode of action of 82D6A3 at the molecular level, we resolved its crystal structure in complex with the A3-domain and fine mapped its paratope by construction and characterization of 13 mutants. The paratope predominantly consists of two short sequences in the heavy chain CDR1 (Asn-31 and Tyr-32) and CDR3 (Asp-99, Pro-101, Tyr-102 and Tyr-103), forming one patch on the surface of the antibody. Trp-50 of the heavy and His-49 of the light chain, both situated adjacent to the patch, play ancillary roles in antigen binding. The crystal structure furthermore confirms the epitope location, which largely overlaps with the collagen binding site deduced from mutagenesis of the A3-domain (Romijn, R. A., Westein, E., Bouma, B., Schiphorst, M. E., Sixma, J. J., Lenting, P. J., and Huizinga, E. G. (2003) J. Biol. Chem. 278, 15035-15039). We herewith further consolidate the location of the collagen binding site and reveal that the potent action of the antibody is due to direct competition for the same interaction site. This information allows the design of a paratope-mimicking peptide with antithrombotic properties.     

Analysis of Dihydrodipicolinate Synthase Promoter Activity in Arabidopsis thaliana by In-Planta Transformation

The present study was carried out to analyze the dihydrodipicolinate synthase (dhdps) gene promoter activity by tracing the GUS expression in tissues and in organs of Arabidopsis thaliana by in planta transformation. The Agrobacterium construct pBI101 used in the studies consists of the reporter gene gus under the control of Arabidopsis thaliana dhdps promoter with 3’ nos controlling sequences and nptll gene under the control of nos promoter and nos terminator. GUS expression in transformed Arabidopsis thaliana was found to be cell type-specific and expressed mainly in the fast growing tissues, where the protein synthesis is high. The histochemical analysis results indicate that the GUS expression was mainly observed in root meristem (elongation zone), emerging lateral roots and in the leaf vascular tissues. In reproductive organs, the GUS expression was observed in anthers, pollen grains and young immature embryos. Southern blot analysis results of T₂, progeny showed the presence of a single integration locus for both the nptll and dhdps promoter.The segregation analysis results showed that the kanamycin resistance gene has not followed the normal Mendelian inheritance.This might be due to the methylation of the nptll gene in some of the transformants.     

Isolation of a poplar and anArabidopsis thaliana dihydrodipicolinate synthase cDNA clone

A poplar DHDPS cDNA clone has been isolated by functional rescue of thedapA-deficient AT997 mutant ofEscherichia coli. By sequence comparison between the poplar and maize DHDPS cDNAs, two oligonucleotides were designed to perform polymerase chain reaction (PCR) onArabidopsis thaliana genomic DNA. The PCR fragment was subsequently used to isolate anArabidopsis DHDPS genomic and cDNA clone.     

Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning

At present, there is much variability between MALDI-TOF MS methodology for the characterization of bacteria through differences in e.g., sample preparation methods, matrix solutions, organic solvents, acquisition methods and data analysis methods. After evaluation of the existing methods, a standard protocol was developed to generate MALDI-TOF mass spectra obtained from a collection of reference strains belonging to the genera Leuconostoc, Fructobacillus and Lactococcus. Bacterial cells were harvested after 24 h of growth at 28 °C on the media MRS or TSA. Mass spectra were generated, using the CHCA matrix combined with a 50:48:2 acetonitrile:water:trifluoroacetic acid matrix solution, and analyzed by the cell smear method and the cell extract method. After a data preprocessing step, the resulting high quality data set was used for PCA, distance calculation and multi-dimensional scaling. Using these analyses, species-specific information in the MALDI-TOF mass spectra could be demonstrated. As a next step, the spectra, as well as the binary character set derived from these spectra, were successfully used for species identification within the genera Leuconostoc, Fructobacillus, and Lactococcus. Using MALDI-TOF MS identification libraries for Leuconostoc and Fructobacillus strains, 84% of the MALDI-TOF mass spectra were correctly identified at the species level. Similarly, the same analysis strategy within the genus Lactococcus resulted in 94% correct identifications, taking species and subspecies levels into consideration. Finally, two machine learning techniques were evaluated as alternative species identification tools. The two techniques, support vector machines and random forests, resulted in accuracies between 94% and 98% for the identification of Leuconostoc and Fructobacillus species, respectively.     

Biochemical Characterisation and Cloning of α-Kafirin Gene from Sorghum (Sorghum bicolor L Moench)

Seed storage proteins from naturally occurring lysine-rich cultivars namely IS 217O₂, CVS 365, G 1058, G 205 and CVS 549 were analyzed biochemically, immunologically and compared with a low-lysine cultivar (White Martin) and a chemically induced high-lysine mutant (P7210). Protein fractionation studies indicated that the high lysine cultivars contained 25% less kafirin and an increased alcohol insoluble reduced glutelin without affecting the total protein content. SDS-PAGE analysis of total kafirin showed the absence of 25.3 kD and 25.9 kD a-kafirin proteins in lysine-rich cultivars IS 217O₂, CVS 365 and G 1058, while in G 205 only the 25.9 kD protein was absent compared to low-lysine cultivar White Martin. A genomic clone λGK5 encoding an a-kafirin has been isolated from cv White Martin genomic library using pSKR3 as hybridizing probe and sequenced. Transient expression studies by particle bombardment of immature seeds of sorghum allowed to detect β-glucuronidase (GUS) activity only in endosperm cells confirming that the α-kafirin gene promoter is functional and tissue specific.