Integration of exogenous DNA into the genome of Azotobacter vinelandii

The soil bacterium Azotobacter vinelandii was genetically transformed by chromosomal integration to ampicillin and/or tetracycline resistance using restriction endonuclease-linearized plasmids. Polyacrylamide gel electrophoresis of protein extracts from three independently isolated ampicillin resistant transformants showed the presence of a 28 Kd band which is the approximate size of the ampicillin resistance gene product (i.e., -lactamase). Moreover, with nitrocefin, a chromogenic cephalosporin, as a substrate, it was shown that all of the ampicillin resistant transformants produced functional -lactamase. DNA hybridization showed that the chromosomal DNA from transformed cells contained plasmid DNA sequences at discrete sites. Growth experiments indicated that stable A. vinelandii transformants that carry functional integrated DNA were physiologically impaired.     

Experimental Evolution of Gene Duplicates in a Bacterial Plasmid Model

The fate of gene duplicates subjected to diversifying selection was tested experimentally in a bacterial system. The wild-type TEM-1 β-lactamase gene confers resistance to ampicillin but not to cefotaxime. Point mutations confer cefotaxime resistance, but they compromise ampicillin resistance. Thus, selection for both drug resistances in a bacterium with two copies of β-lactamase should favor the divergence of one copy to improve cefotaxime resistance while maintaining the other copy to preserve ampicillin resistance. This selection was performed on a bacterium with identical sequences of β-lactamase on two separate, compatible plasmids. As expected, one plasmid evolved increased cefotaxime resistance when appropriately strong cefotaxime selection was applied. However, the cefotaxime-resistant plasmid maintained sufficient ampicillin resistance to tolerate the concentration of ampicillin used, and the other plasmid was lost. Hosts carrying both the cefotaxime-resistant and wild-type plasmids were then subjected to various higher concentrations of both drugs to find conditions that would ensure the maintenance of both plasmids. In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow. This study highlights the importance of the cost of duplicate genes and the quantitative nature of the tradeoff in the evolution of gene duplication through functional divergence. Reviewing Editor: Dr. Margaret Riley     

Rapid detection and identification of the bacterium Pantoea stewartii in maize by TaqMan real-time PCR assay targeting the cpsD gene

Aims: The development and evaluation of a sensitive and specific TaqMan^® real-time polymerase chain reaction (PCR) for the detection and identification of Pantoea stewartii on maize. Methods and Results: A TaqMan^®-based real-time PCR assay targeting the cpsD gene enabling specific detection of P. stewartii in maize leaves and seeds was developed. Under optimal conditions, the selected primers and probe were specific for the detection of all 14 reference P. stewartii strains by real-time PCR. The 32 non-Panteoa and eight other Pantoea strains tested negative. The TaqMan^® PCR assay detected 1 pg of purified DNA and 10⁴P. stewartii colony forming units per millilitre (10 cells per reaction) in pure cultures consisting of 92·0% intact (viable) cells. Direct processing of leaf lesions and seeds by the real-time PCR detected 10 and 50 P. stewartii cells per reaction respectively. TaqMan^® real-time PCR results were validated by dilution plating of macerates and PCR-based subcloning followed by DNA sequencing. Conclusions: The real-time PCR assay described is a rapid, reliable and more sensitive tool for the detection of P. stewartii. Significance and Impact of the study: This real-time PCR assay would avoid false-negative results and reduce the time required for certifying maize seed shipments.     

Miniprimer PCR assay targeting multiple genes: a new rapid and reliable tool for genotyping Pantoea stewartii subsp. stewartii

Aim: Development of a ‘miniprimer’ PCR assay for genotyping Pantoea stewartii subsp. stewartii, the causal agent of the Stewart’s bacterial wilt on maize. Methods and Results: Four 10‐nucleotide (10‐nt) ‘miniprimer’ sets were designed and evaluated in the presence of Titanium Taq DNA polymerase. Under optimal reaction conditions, the miniprimer pair Uni‐BacF‐10/Uni‐BacR‐10 reproducibly generated identical banding patterns among 10 strains of P. stewartii subsp. stewartii, different patterns from strains of P. stewartii subsp. indologenes, other Panteoa species, Clavibacter michiganensis, Pectobacterium spp., Pseudomonas spp. and other bacterial species. The amplicons of Pantoea stewartii subsp. stewartii were cloned and sequenced to identify genes or DNA fragments that are targeted by the miniprimer PCR assay. Of the 14 ‘clone types’ identified, sequences of a 1·23‐kb fragment had a 99·8% similarity to part of the Pantoea stewartii zeaxanthin diglucoside biosynthetic operon ( AY166713 ). Other dominant cloned fragments included a 411‐bp amplicon that exhibited 99·8% similarity to the psaU gene (syn:ysaU; GQ249669 ), a type III protein‐secretion system complex of P. stewartii subsp. stewartii strain DC283, and a 548‐bp fragment showed 63% homology to the Asp/Glu racemase encoding gene in Erwinia tasmaniensis strain ET1/99. Conclusion: The miniprimer PCR assay reported here is highly discriminatory and reproducible in genotyping Pantoea stewartii subsp. stewartii. Significance and Impact of the study: This miniprimer PCR assay could be a new reliable and rapid tool for fingerprinting the Stewart’s wilt pathogen of maize.     

Pantoea stewartii Causing Stewart's Wilt on Dracaena sanderiana in Korea

In April 2010, a severe occurrence of Stewart's wilt on Dracaena sanderiana plants was observed in greenhouses in Seongnam, Gyeonggi Province, South Korea, with an incidence of 35‐50%. Being imported plants, little was known about the pathogens associated with D. sanderiana. Symptoms included chlorosis, wilting and leaf blight on the leaf surfaces. Physiological analysis, pathogenicity tests, sequencing and phylogenetic analysis of the 16S rRNA gene revealed that the pathogen was the bacterium Pantoea stewartii. To the best of our knowledge, this is the first report on bacterial wilt caused by P. stewartii on D. sanderiana.     

Development and evaluation of a real‐time PCR assay targeting chromosomal DNA of Erwinia amylovora

Aims:  To develop and evaluate a new and reliable real‐time PCR detection protocol on chromosomal DNA of the contagious plant pathogenic bacterium Erwinia amylovora, the causal agent of fire blight. Methods and Results:  A Taqman^® minor‐groove‐binder real‐time PCR assay targeting a hypothetical protein coding gene of Erw. amylovora has been developed. Colony PCR of 113 bacterial strains from different taxa was performed to prove specificity. Serial decimal dilutions of Erw. amylovora showed a consistent detection sensitivity of 2 bacterial units per μl. All strains of Erw. amylovora could be identified, and there were no cross‐reactions with matrices or other bacteria also testing naturally contaminated samples. Conclusions:  Rapid, reliable and sensitive detection of Erw. amylovora is important to avoid the spread of the disease within orchards, and the distribution by contaminated plant material or vectors carrying the pathogen. The selected conserved target gene allows relative quantitative detection of Erw. amylovora from different sources and host taxa. The newly developed protocol also enables the detection of recently found natural strains that lack the species‐specific plasmid pEA29, which was so far widely used as target for detection and identification of this plant pathogen by PCR. Significance and Impact of the Study:  This study demonstrates that the newly developed and evaluated real‐time assay can specifically be used for identifying all known strains of the EU quarantine plant pathogen Erw. amylovora. Low concentrations of the bacteria can be detected and relatively quantified using a different target area than other real‐time PCRs designed so far.     

Heterogeneity in the level of ampicillin resistance conferred by pBR322 derivatives with different DNA supercoiling

Summary Cloning of an EcoRI restriction fragment, containing the 900 bp -terminal sequence of transposon Tn1000, into pBR322, resulted in two plasmids, pICV63 and pICV64, which differed in the orientation of the cloned fragment within the replicon and in the level of ampicillin resistance conferred on the host cell. The DNAs of these plasmids differ in superhelicity and we suggest that a change in supercoiling of pICV63 DNA leads to this plasmid conferring resistance to only low levels of ampicillin, probably by reducing the expression of the bla gene. This hypothesis is supported by the fact that topA or supX mutations, which abolish topoisomerase I, reduce still further the level of resistance to ampicillin of pICV63-containing cells, whereas the gyrB226 compensatory mutation renders these cells more ampicillin resistant. Plasmid pICV63, therefore, enables mutant alleles of genes governing DNA topology to be recognized.     

Retrofitting ampicillin resistant vectors by recombination for use in generating C. elegans transgenic animals by bombardment

Caenorhabditis elegans is an important model organism for modern biologic research. An essential aspect of C. elegans research is the production of transgenic animals for study. These are often generated via microinjection, but biolistic bombardment has become increasingly popular. However, many of the plasmids previously generated for use in microinjection are not readily used for bombardment due to the lack of a convenient marker. The unc-119 gene is often used as a marker since unc-119 rescue can be observed at low magnification, allowing rescued animals to be easily distinguished from the larger number of non-rescued animals. Here we report the use of homologous recombination in Escherichia coli as a method to insert a cassette containing the unc-119 gene into commonly used plasmids at the site of the ampicillin resistance gene which is simpler than other methods like subcloning. These cassettes are flanked by regions homologous to the 5′ and 3′ ends of the ampicillin resistance gene and contain either the unc-119 gene and the kanamycin resistance gene or a unc-119:mCherry fusion gene and the kanamycin resistance gene. The resulting plasmids may be used for biolistic bombardment to yield animals that display unc-119 rescue, and also express the recipient plasmid transgene.     

Identification of the aph IV gene from protoplast-derived maize plants by a simple nonradioactive DNA hybridization method

Summary Protoplast-derived, transformed maize plants were evaluated by Southern analysis for the presence of the aph IV gene which codes for resistance to the antibiotic, hygromycin B. This gene was used as a selectable marker for the transformation of maize protoplasts. Southern analysis was performed with fluorescein-labeled probe DNA. A new method for labeling molecular weight markers with fluorescein-N⁶ is presented. The nonradioactive Southern analysis method is compared to the radioactive method and the results show that the nonradioactive method is as sensitive as the radioactive method.     

Inducible nickel resistance in a river isolate of India phylogenetically ascertained as a novel strain of Acinetobacter junii

Summary A gram negative, motile, short rod-shaped, and nickel resistant (tolerating 6.5 mM Ni²⁺) bacterium, strain BB1A, was isolated from the waters of the River Torsa in Hashimara, Jalpaiguri district, West Bengal, India. The isolate BB1A was identified as a strain of Acinetobacter junii following detailed analysis of morphological, physio-biochemical and 16S rRNA gene sequence. The expression of nickel resistance in BB1A was inducible by exposure to nickel chloride at a concentration as low as 50 μM Ni²⁺. The other metal ions, Cu²⁺, Zn²⁺, or Pb²⁺ at a concentration range of 20–30 μM, also induced the nickel resistance system in this bacterium. Southern hybridizations of BB1A genomic DNA with digoxigenin-dUTP labeled DNA probes specific for well known nickel resistance determinants, cnr, ncc or nre, resulted in no detectable signal, but nir specific probe yielded weak hybridization signal with restricted genomic DNA of BB1A. The isolate BB1A, therefore, carries out a novel induction phenomenon of nickel resistance and presumably with a nickel resistance genetic system different from that previously characterized in other bacteria.     

Attempts to transform Zea mays via pollen grains

Summary An attempt was made to transfer two sorts of DNA into maize via pollen grains. Controls for both pollen quality and DNA behaviour during the transformation experiments were included. When genomic DNA was used, no transformants were observed among the 1805 seeds screened. With plasmid DNA (harbouring the gene expressing kanamycin resistance in plant cells), three plants with kanamycin resistance were observed among the 1723 seeds screened, although no molecular evidence of transformation was obtained. Experiments indicated that under the conditions used, DNA was being degraded by both pollen and stigma nucleases. Consequently, we attempted to determine protocols which would inhibit these nuclease activities in order to preserve DNA integrity during transformation experiments, thus allowing fertilization. We found that a classic germination medium supplemented by 300 or 600 mM KNO₃, or 20% PEG₁₅₅₀ satisfied all these conditions.Abbreviations BK Brewbaker and Kwack medium - BKS15 Brewbaker and Kwack medium containing 15% (w/v) sucrose - EDTA ethyldiaminetetraacetic acid - FCR fluorochromatic reaction - FP fertilization percentage - PEG polyethylene-glycol     

Structure and expression of the lignin O-methyltransferase gene from Zea mays L.

The isolation and characterization of cDNA and homologous genomic clones encoding the lignin O-methyltransferase (OMT) from maize is reported. The cDNA clone has been isolated by differential screening of maize root cDNA library. Southern analysis indicates that a single gene codes for this protein. The genomic sequence contains a single 916 bp intron. The deduced protein sequence from DNA shares significant homology with the recently reported lignin-bispecific caffeic acid/5-hydroxyferulic OMTs from alfalfa and aspen. It also shares homology with OMTs from bovine pineal glands and a purple non-sulfur photosynthetic bacterium. The mRNA of this gene is present at different levels in distinct organs of the plant with the highest accumulation detected in the elongation zone of roots. Bacterial extracts from clones containing the maize OMT cDNA show an activity in methylation of caffeic acid to ferulic acid comparable to that existing in the plant extracts. These results indicate that the described gene encodes the caffeic acid 3-O-methyltransferase (COMT) involved in the lignin biosynthesis of maize.     

Agrobacterium-mediated transformation of maize (Zea mays) with Cre-lox site specific recombination cassettes in BIBAC vectors

The Cre/loxP site-specific recombination system has been applied in various plant species including maize (Zea mays) for marker gene removal, gene targeting, and functional genomics. A BIBAC vector system was adapted for maize transformation with a large fragment of genetic material including a herbicide resistance marker gene, a 30 kb yeast genomic fragment as a marker for fluorescence in situ hybridization (FISH), and a 35S-lox-cre recombination cassette. Seventy-five transgenic lines were generated from Agrobacterium-mediated transformation of a maize Hi II line with multiple B chromosomes. Eighty-four inserts have been localized among all 10 A chromosome pairs by FISH using the yeast DNA probe together with a karyotyping cocktail. No inserts were found on the B chromosomes; thus a bias against the B chromosomes by the Agrobacterium-mediated transformation was revealed. The expression of a cre gene was confirmed in 68 of the 75 transgenic lines by a reporter construct for cre/lox mediated recombination. The placement of the cre/lox site-specific recombination system in many locations in the maize genome will be valuable materials for gene targeting and chromosome engineering.     

Production of herbicide-resistant transgenic maize plants using electroporation of seed-derived embryos

The improvement of commercial maize lines via biotechnological approaches is limited by the lack of a transformation system that is tissue culture free. In this paper, the development of a genetic transformation system is presented using electroporation for gene delivery and seed-derived embryo as the gene target. Plasmid DNA (pBARGUS), which contained the selectablebar gene for resistance to the herbicide Basta and the screenablegus gene, was delivered into enzymatically wounded mature maize embryos via electroporation. Transformed plants were identified by their ability to grow on a selective medium containing 30 mg/L of phosphinothricin. Southern hybridization, plant resistance to the application of Basta, GUS expression, and segregation analysis indicated that a functionalbar gene had integrated into the maize genome and was inherited in a mendelian fashion by the progeny.     

Analysis of a novel class 1 integron containing metallo-β-lactamase gene VIM-2 in <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis>

Carbapenems such as imipenem are stable to most β-lactamases. Recently, increased numbers of carbapenemase producing Gram-negative bacterial strains have been isolated because of the increased use of cabapenems. In this respect, control of these infectious carbapenemase producing Gram-negative bacteria and understanding their resistance mechanism are becoming more important. These carbapenem-hydrolyzing β-lactamase genes have been reported to exist mostly as gene cassettes in an integron. This implies that antibiotic resistance genes may be transferred to other bacteria via the integron. In the present study, we identified and analyzed an integron containing VIM-2 type metallo-β-lactamase gene in a carbapenemase producing Pseudomonas aeruginosa. In addition, the possibility of resistance spread by integron located in a plasmid was tested. Among glucose non-fermenting Gram-negative bacilli with reduced imipenem susceptibility (MIC≥8 μg/ml) isolated from Korean patients, P. aeruginosa 1082 showed resistance to most β-lactams, cephalosporin, and aminoglycoside. We found that P. aeruginosa 1082 was inhibited by EDTA in EDTA double disk synergy test which means that this strain produces metallo-β-lactamase. Class 1 integron containing bla _VIM-2 (carbapenem resistance gene), qacF (quaternary ammonium compound resistance gene), aacA4 (aminoglycoside resistance gene), catB3 (chloramphenicol resistance gene), bla _oxa-30 (extended-spectrum β-lactam resistance gene), and aadAl (aminoglycoside resistance gene) gene cassettes was detected in P. aeruginosa 1082. The size of the integron was 5,246 bp and the structure and arrangement of the integron was a novel one in comparison with other integrons found in other P. aeruginosa. The integron could be transferred to Escherichia coli JM109 from P. aeruginosa 1082 possibly via self-transferable plasmid DNA. The integron and a bla _VIM-2 gene were detected in the plasmid DNA of the transconjugants whose imipenem resistance was slightly increased as a result of accepting the integron from the donor strain.     

Characterization and fine mapping of <Emphasis Type="Italic">RppQ</Emphasis>, a resistance gene to southern corn rust in maize

Southern corn rust (SCR) is a fungal disease caused by Puccinia polysora Underw, which can infect maize and may result in substantial yield losses in maize production. The maize inbred line Qi319 carries the SCR resistance gene RppQ. In order to identify molecular markers linked to the RppQ gene, several techniques were utilized including random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), and amplified fragment length polymorphism (AFLP). In addition, sequence characterized amplified region (SCAR) techniques combined with bulked segregant analysis (BSA) were used. Seven RAPD markers, eight SSR markers, and sixty-three AFLP primer combinations amplified polymorphisms between two parents and two bulk populations. A large F₂ population was used for genetic analysis and for fine mapping of the RppQ gene region. One AFLP polymorphic band, M-CAA/E-AGC₃₂₄, was converted to a SCAR marker, MA7, which was mapped to a position 0.46 cM from RppQ. Finally, the RppQ gene was mapped between the SCAR marker MA7 and the AFLP marker M-CCG/E-AGA₁₅₇ with distances of 0.46 and 1.71 cM, respectively.     

An Improved pPZP Vector for Agrobacterium-mediated Plant Transformation

We report a new and improved pPZP vector (pPZP3425) for efficient plant transformation. This vector is derived from the widely used pPZP100 series of binary Agrobacterium vectors. One disadvantage of these vectors is the use of chloramphenicol resistance for selection in Escherichia coli and Agrobacteria. We have therefore included a kanamycin resistance gene for selection in Agrobacterium. Furthermore, the strong 35S CaMV promoter driving the plant resistance gene has been replaced by the weaker nos promoter because it has been shown that the 35S promoter driving the plant resistance marker can lead to ectopic expression of the transgene. During replacement of the 35S promoter, the NcoI site within the plant resistance gene has been removed, and NcoI can now be used for cloning purposes within the expression cassette which consists of an intron-containing gus gene driven by a strong constitutive promoter (35S promoter with doubled enhancer plus omega-element as translational enhancer). Thus, a single vector can conveniently be used for two purposes: (1) for overexpression of proteins by replacing the gus gene by the coding sequence of choice and (2) for creation of promoter:gus fusions by substituting the constitutive promoter by any other promoter. We demonstrate the usefulness of this vector for cloning a promoter:gus fusion and in planta transformation of Arabidopsis.     

Targeted mutagenesis in the progeny of maize transgenic plants

We have demonstrated that targeted mutagenesis can be accomplished in maize plants by excision, activation, and subsequent elimination of an endonuclease in the progeny of genetic crosses. The yeast FLP/FRT site-specific recombination system was used to excise and transiently activate the previously integrated yeast I-SceI homing endonuclease in maize zygotes and/or developing embryos. An artificial I-SceI recognition sequence integrated into genomic DNA was analyzed for mutations to indicate the I-SceI endonuclease activity. Targeted mutagenesis of the I-SceI site occurred in about 1% of analyzed F1 plants. Short deletions centered on the I-SceI-produced double-strand break were the predominant genetic lesions observed in the F1 plants. The I-SceI expression cassette was not detected in the mutant F1 plants and their progeny. However, the original mutations were faithfully transmitted to the next generation indicating that the mutations occurred early during the F1 plant development. The procedure offers simultaneous production of double-strand breaks and delivery of DNA template combined with a large number of progeny plants for future gene targeting experiments.     

Introduction and constitutive expression of a tobacco hornworm (<Emphasis Type="Italic">Manduca sexta</Emphasis>) chitinase gene in soybean

Summary Embryogenic soybean [Glycine max (L.) Merrill] cultures were transformed with a Manduca sexta chitinase (msc) gene using microprojectile bombardment. A 1.7 kb DNA fragment encoding a tobacco hornworm chitinase was cloned into the rice transformation vector pGL2, under the control of the maize ubiquitin promoter and linked to the hpt gene as a selectable marker. After bombardment, hygromycin-resistant tissues were isolated and cultured to give rise to clones of transgenic material. Four hygromycin-resistant clones were converted into plants. Two clones were positive for the msc gene via polymerase chain reaction (PCR) and Southern blot analysis. The integration inheritance, and expression of transgenes were confirmed by molecular analysis of transgenic soybean plants. Progeny analysis showed that the introduced genes were inherited and segregated in a 3:1 Mendelian fashion. DNA blot experiments and progeny inheritance analysis indicated that the plants contained several copies of the msc gene and that the insertion occurred at a single locus. Northern blotting analysis confirmed the expression of the transgenes. Western blot analysis of transgenic plants and their progeny revealed the presence of a protein with a molecular weight of 48kDa that reacted with the Manduca sexta antibody. Progeny from the chitinase-positive plants were tested for their resistance to the soybean cyst nematode. Plants expressing the insect chitinase did not manifest enhanced resistance to the soybean cyst nematode.