Genetics of avirulence genes in Blumeria graminis f.sp. hordei and physical mapping of AVR(a22) and AVR(a12).

Powdery mildew fungi are parasites that cause disease on a wide range of important crops. Plant resistance (R) genes, which induce host defences against powdery mildews, encode proteins that recognise avirulence (AVR) molecules from the parasite in a gene-for-gene manner. To gain insight into how virulence evolves in Blumeria graminis f.sp. hordei, associations between segregating AVR genes were established. As a prerequisite to the isolation of AVR genes, two loci were selected for further analysis. AVR(a22) is located in a tightly linked cluster comprising AVR(a10) and AVR(k1) as well as up to five other AVR genes. The ratio between physical and genetic distance in the cluster ranged between 0.7 and 35 kB/cM. The AVR(a22) locus was delimited by the previously isolated gene AVR(a10) and two cleaved amplified polymorphic sequence (CAPS) markers, 19H12R and 74E9L. By contrast, AVR(a12) was not linked to other AVR genes in two crosses. Bulk segregant analysis of over 100,000 AFLP fragments yielded two markers, ETAMTG-285 and PAAMACT-473, mapping 10 and 2cM from AVR(a12), respectively, thus delimiting AVR(a12) on one side. All markers obtained for AVR(a12) mapped proximal to it, indicating that the gene is located at the end of a chromosome. Three more AVR(a10) paralogues were identified at the locus interspersed among genes for metabolic enzymes and abundant repetitive elements, especially those homologous to the CgT1 class of retrotransposons. The flanking and close markers obtained will facilitate the isolation of AVR(a22) and AVR(a12) and provide useful tools for studies of the evolution of powdery mildew fungi in agriculture and nature.     

Dealing with virtual aggregation – a new index for analysing heterogeneous point patterns

Point pattern analyses such as the estimation of Ripley's K‐function or the pair‐correlation function g are commonly used in ecology to characterise ecological patterns in space. However, a major disadvantage of these methods is their missing ability to deal with spatial heterogeneity. A heterogeneous intensity of points causes a systematic bias in estimates of the K‐ and g‐functions, a phenomenon termed “virtual aggregation” in the recent literature. To address this problem, we derive a new index, called K2‐index, as an extension of existing point pattern characteristics. The K2‐index has a heuristic interpretation as an approximation to the first derivative of the g‐function. We estimate the K‐, g‐ and K2‐functions for six different types of simulated point patterns and show that the K2‐index may provide important information on point patterns that the other methods fail to detect. The results indicate that particularly the small‐scale distributions of points are better represented by the K2‐index. This might be important for testing hypotheses on ecological processes, because most of these processes, such as direct neighbour interactions, occur very locally. When applied to empirical patterns of molehill distribution, the results of the K2‐analysis show regularity up to distances between 0.1 and 0.4 m in most of the study areas, and aggregation of molehills up to distances between 0.2 and 1.1 m. The type and scale of these deviations from randomness agree with a priori expectations on the hill‐building behaviour of moles. In contrast, the estimated g‐functions merely indicate aggregation at the full range from 0 to 7 m (or even above). Considering the advantages and disadvantages of the different methods, we suggest that the K2‐index should be used as a complement to existing approaches, particularly for point patterns generated by processes that act on more than one scale.     

Transient transfection of Echinococcus multilocularis primary cells and complete in vitro regeneration of metacestode vesicles

A major limitation in studying molecular interactions between parasitic helminths and their hosts is the lack of suitable in vitro cultivation systems for helminth cells and larvae. Here we present a method for long-term in vitro cultivation of larval cells of the tapeworm Echinococcus multilocularis, the causative agent of alveolar echinococcosis. Primary cells isolated from cultivated metacestode vesicles in vitro showed a morphology typical of Echinococcus germinal cells, displayed an Echinococcus-specific gene expression profile and a cestode-like DNA content of approximately 300Mbp. When kept under reducing conditions in the presence of Echinococcus vesicle fluid, the primary cells could be maintained in vitro for several months and proliferated. Most interestingly, upon co-cultivation with host hepatocytes in a trans-well system, mitotically active Echinococcus cells formed cell aggregates that subsequently developed central cavities, surrounded by germinal cells. After 4 weeks, the cell aggregates gave rise to young metacestode vesicles lacking an outer laminated layer. This layer was formed after 6 weeks of cultivation indicating the complete in vitro regeneration of metacestode larvae. As an initial step toward the creation of a fully transgenic strain, we carried out transient transfection of Echinococcus primary cells using plasmids and obtained heterologous expression of a reporter gene. Furthermore, we successfully carried out targeted infection of Echinococcus cells with the facultatively intracellular bacterium Listeria monocytogenes, a DNA delivery system for genetic manipulation of mammalian cells. Taken together, the methods presented herein constitute important new tools for molecular investigations on host-parasite interactions in alveolar echinococcosis and on the roles of totipotent germinal cells in parasite regeneration and metastasis formation. Moreover, they enable the development of fully transgenic techniques in this group of helminth parasites for the first time.     

Community dynamics within a bacterial consortium during growth on toluene under sulfate-reducing conditions

A sulfate-reducing bacterial consortium was enriched from an anoxic aquifer contaminated with BTEX compounds, using toluene as a growth substrate. Total cell counts, protein contents and sulfide production were determined to follow growth at the in situ temperature (14 °C) and at 25 °C, respectively. Community members were identified by 16S rRNA gene cloning and sequencing. Phylogenetic analysis revealed 12 sequence types belonging to Deltaproteobacteria (several groups) , Epsilonproteobacteria, Bacteroidetes, Spirochaetaceae and an unclassified bacterial clade. The most prominent phylotype comprising 34% of all clones was affiliated to the Desulfobulbaceae and closely related to environmental clones retrieved from hydrocarbon-contaminated aquifers. Flow-cytometric methods were applied to analyze the community dynamics and to identify key organisms involved in toluene assimilation. Flow-cytometric measurement of DNA contents and scatter behavior served to detect and quantify dominant and newly emerging clusters of subcommunities. Up to seven subcommunities, two of them dominant, were distinguished. Cell sorting was used to facilitate the analysis of conspicuous clusters for phylogenetic identity by terminal restriction fragment length polymorphism profiling of the 16S rRNA genes. The Desulfobulbaceae phylotype accounted for up to 87% in proliferating subcommunities, indicating that it represents the key organism of toluene degradation within this complex anaerobic consortium.     

Sinapoyltransferases in the light of molecular evolution

Acylation is a prevalent chemical modification that to a significant extent accounts for the tremendous diversity of plant metabolites. To catalyze acyl transfer reactions, higher plants have evolved acyltransferases that accept β-acetal esters, typically 1-O-glucose esters, as an alternative to the ubiquitously occurring CoA-thioester-dependent enzymes. Shared homology indicates that the β-acetal ester-dependent acyltransferases are derived from a common hydrolytic ancestor of the Serine CarboxyPeptidase (SCP) type, giving rise to the name Serine CarboxyPeptidase-Like (SCPL) acyltransferases. We have analyzed structure–function relationships, reaction mechanism and sequence evolution of Arabidopsis 1-O-sinapoyl-β-glucose:l-malate sinapoyltransferase (AtSMT) and related enzymes to investigate molecular changes required to impart acyltransferase activity to hydrolytic enzymes. AtSMT has maintained the catalytic triad of the hydrolytic ancestor as well as part of the H-bond network for substrate recognition to bind the acyl acceptor l-malate. A Glu/Asp substitution at the amino acid position preceding the catalytic Ser supports binding of the acyl donor 1-O-sinapoyl-β-glucose and was found highly conserved among SCPL acyltransferases. The AtSMT-catalyzed acyl transfer reaction follows a random sequential bi-bi mechanism that requires both substrates 1-O-sinapoyl-β-glucose and l-malate bound in an enzyme donor–acceptor complex to initiate acyl transfer. Together with the strong fixation of the acyl acceptor l-malate, the acquisition of this reaction mechanism favours transacylation over hydrolysis in AtSMT catalysis. The model structure and enzymatic side activities reveal that the AtSMT-mediated acyl transfer proceeds via a short-lived acyl enzyme complex. With regard to evolution, the SCPL acyltransferase clade most likely represents a recent development. The encoding genes are organized in a tandem-arranged cluster with partly overlapping functions. With other enzymes encoded by the respective gene cluster on Arabidopsis chromosome 2, AtSMT shares the enzymatic side activity to disproportionate 1-O-sinapoyl-β-glucoses to produce 1,2-di-O-sinapoyl-β-glucose. In the absence of the acyl acceptor l-malate, a residual esterase activity became obvious as a remnant of the hydrolytic ancestor. With regard to the evolution of Arabidopsis SCPL acyltransferases, our results suggest early neofunctionalization of the hydrolytic ancestor toward acyltransferase activity and acyl donor specificity for 1-O-sinapoyl-β-glucose followed by subfunctionalization to recognize different acyl acceptors.