Structure and substrate specificity of acetyltransferase ACIAD1637 from Acinetobacter baylyi ADP1

Gene ACIAD1637 from Acinetobacter baylyi ADP1 encodes a 182 amino acid putative antibiotic resistance protein. The structure of this protein (termed acepita) has been solved in space group P₂ to 2.35 Å resolution. Acepita belongs to the GCN5-related N-acetyltransferase (GNAT) family, and contains the four sequence motifs conserved among family members. The structure of acepita is compared with that of pita, its homologue from Pseudomonas aeruginosa. Acepita has a similar substrate profile to pita and performs a similar function.     

Utility of barley and wheat simple sequence repeat (SSR) markers for genetic analysis of Hordeum chilense and tritordeum

A selection of 36 wheat and 35 barley simple sequence repeat markers (SSRs) were studied for their utility in Hordeum chilense. Nineteen wheat and nineteen barley primer pairs amplified consistent H. chilense products. Nine wheat and two barley SSRs were polymorphic in a H. chilense mapping population, producing codominant markers that mapped to the expected homoeologous linkage groups in all but one case. Thirteen wheat and 10 barley primer pairs were suitable for studying the introgression of H. chilense into wheat because they amplified H. chilense products of distinct size. Analysis of wheat/H. chilense addition lines showed that the H. chilense products derived from the expected homoeologous linkage groups. The results showed that wheat and barley SSRs provide a valuable resource for the genetic characterization of H. chilense, tritordeums and derived introgression lines. Received: 20 November 2000 / Accepted: 12 April 2001     

The effect of additional virulence genes on transformation efficiency,transgene integration and expression in rice plants using the pGreen/pSoup dual binary vector system

We assessed the effect of four different virulence (vir) gene combinations on plant transformation efficiency and transgene behaviour in rice using the pGreen/pSoup dual binary vector system. Transformation experiments were conducted using a pGreen vector containing the bar and gusA expression units with, or without, the virG542, virGN54D, virGwt or the virG/B/C genes added to the backbone. Additonal vir gene(s) significantly altered plant transformation efficiency and the integration of vector backbone sequences. However, no differences in transgene copy number, percentage of expressing lines and expression levels could be detected. Addition of virGwt was the most beneficial, doubling the overall performance of the pGreen/pSoup vector system based on transformation frequency, absence of backbone sequence integration and expression of unselected transgenes. In 39 of the plant lines, the additional vir genes were integrated into the rice genome. The contribution of super dual binary pGreen/pSoup vectors to the development of efficient rice transformation systems and to the production of plants free of selectable marker genes are discussed.     

Strategies for precise quantification of transgene expression levels over several generations in rice

Variation in transgene expression levels can result from uncontrolled differences in experimental protocols. Studies conducted over generations could, by their design, generate additional unwanted variation. To study sources of spurious variation, transgene expression levels were quantified over five homozygous generations in two independent transgenic rice lines created by particle bombardment. Both lines contained the same gus expression unit and had been shown to exhibit stable inheritance of transgene structure and expression. All plants were cultured and sampled using previously developed standardized protocols. Plants representative of each generation (T2, T3, T4, T5, T6) were grown either all together or across several different growth periods. GUS activity in plants from different generations was quantified either in the same assay or over multiple independent assays. Strategies in which plants were grown and phenotyped independently, significantly increased (up to 3-fold) extraneous variation in transgene expression level quantification, thus reducing the precision of molecular genetic studies and generating artefactual results in transgenic studies conducted over generations. Identification of sources of unwanted variation and quantification of their effect allowed the development of new strategies designed to control spurious variation. Growth and phenotyping of all plants from all generations together, using standard operating procedures (SOP), led to a reduction in extraneous variation associated with transgene expression level quantification. Adoption of such strategies is key to improving the reproducibility of transgenic studies conducted over generations.     

Development of a rapid assay for determining the relative abundance of bacteria

A sandwich hybridization assay for high-throughput, rapid, simple, and inexpensive quantification of specific microbial populations was evaluated. The assay is based on the hybridization of a target rRNA with differentially labeled capture and detector probes. Betaproteobacterial ammonia-oxidizing bacteria (AOB) were selected as the target group for the study, since they represent a phylogenetically coherent group of organisms that perform a well-defined geochemical function in natural and engineered environments. Reagent concentrations, probe combinations, and washing, blocking, and hybridization conditions were optimized to improve signal and reduce background. The detection limits for the optimized RNA assay were equivalent to approximately 10(3) to 10(4) and 10(4) to 10(5) bacterial cells, respectively, for E. coli rRNA and RNA extracted from activated sludge, by using probes targeting the majority of bacteria. Furthermore, the RNA assay had good specificity, permitted discrimination of rRNA sequences that differed by a 2-bp mismatch in the probe target region, and could distinguish the sizes of AOB populations in nitrifying and nonnitrifying wastewater treatment plants.     

Intrachromosomal mapping of the nucleolar organiser region relative to three marker loci on chromosome 1B of wheat (Triticum aestivum)

Summary Restriction enzyme digestion of the ribosomal RNA genes of the nucleolar organisers of wheat has revealed fragment length polymorphisms for the nucleolar organiser on chromosome 1B and the nucleolar organiser on 6B. Variation between genotypes for these regions has also been demonstrated. This variation has been exploited to determine the recombination frequency between the physically defined nucleolar organiser on 1B (designatedNor1) and other markers; two loci,Glu-B1 andGli-B1 which code for endosperm storage proteins andRf3, a locus restoring fertility to male sterility conditioned byT. timopheevi cytoplasm.Gli-B1 andRf3 were located on the short-arm satellite but recombine with the nucleolar organiser giving a gene order ofNor1 — Rf3 — Gli-B1. Glu-B1 is located on the long arm of 1B but shows relatively little recombination withNor1, which is, in physical distance, distal on the short arm. This illustrates the discrepancy between map distance and physical distance on wheat chromosomes due to the distal localisation of chiasmata. The recombination betweenNor1 andRf3 indicates that, contrary to previous suggestions, fertility restoration is not a property of the nucleolar organiser but of a separate locus.