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Biomedical subjects

Philipp Franken

Publications and source records attributed to Philipp Franken.

9 recordsLinked to original sources
PubMed2006

Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.

The great majority of terrestrial plants enters a beneficial arbuscular mycorrhiza (AM) or ectomycorrhiza (ECM) symbiosis with soil fungi. In the SPP 1084 "MolMyk: Molecular Basics of Mycorrhizal Symbioses", high-throughput EST-sequencing was performed to obtain snapshots of the plant and fungal transcriptome in mycorrhizal roots and in extraradical hyphae. To focus activities, the interactions between Medicago truncatula and Glomus intraradices as well as Populus tremula and Amanita muscaria were selected as models for AM and ECM symbioses, respectively. Together, almost, 20.000 expressed sequence tags (ESTs) were generated from different random and suppressive subtractive hybridization (SSH) cDNA libraries, providing a comprehensive overview of the mycorrhizal transcriptome. To automatically cluster and annotate EST-sequences, the BioMake and SAMS software tools were developed. In connection with the eNorthern software SteN, plant genes with a predicted mycorrhiza-induced expression were identified. To support experimental transcriptome profiling, macro- and microarray tools have been constructed for the two model mycorrhizae, based either on PCR-amplified cDNAs or 70mer oligonucleotides. These arrays were used to profile the transcriptome of AM and ECM roots under different conditions, and the data obtained were uploaded to the ArrayLIMS and EMMA databases that are designed to store and evaluate expression profiles from DNA arrays. Together, the EST- and transcriptome databases can be mined to identify candidate genes for targeted functional studies.

Computational Biology↗
PubMed2006

Gene expression analysis of arbuscule development and functioning.

The arbuscular mycorrhiza (AM) is characterized by specific morphological structures of the fungus and the plant and by physiological adaptations which are mostly beneficial for both partners of the symbiosis. This review describes approaches to study the molecular basis of the interaction. RNA accumulation patterns have been monitored in Pisum sativum to analyse the plant response to arbuscule development. In a direct approach, the Mtha1 gene from Medicago truncatula was cloned which is expressed in arbusculated cells of M. truncatula. The gene putatively encodes an H(+)-ATPase involved in the improved plant nutrition during mycorrhization. Finally, a tripartite system between M. truncatula, Glomus mosseae and Aphanomyces euteiches was established, in order to study bioprotection. Analysis of the transcriptome has been started to analyse the interaction between the plant, the pathogen and the AM fungus.

Gene Expression Regulation, Plant↗
PubMed2006

Endophyte or parasite--what decides?

Symbiosis between a fungus and a plant is a widespread phenomenon in nature. The outcome of such an interaction can vary in a seamless manner from mutualism to parasitism. In most cases, the host plant does not suffer, in fact it often gains an advantage from colonization by a fungus. This benefit is based on a fine-tuned balance between the demands of the invader and the plant response. If the interaction becomes unbalanced, disease symptoms appear or the fungus is excluded by induced host defence reactions. Symbioses of plants with beneficial or neutral endophytes share many common attributes with plant interactions with pathogens. Recent findings emerging from studies of compatible host-fungus interactions have enhanced our understanding of what determines whether the fungus behaves as an endophyte or a parasite and of how plants avoid exploitation by detrimental parasites but benefit from mutualistic endophytes.

Fungi↗
PubMed2005

The endophytic fungus Piriformospora indica reprograms barley to salt-stress tolerance, disease resistance, and higher yield.

Disease resistance strategies are powerful approaches to sustainable agriculture because they reduce chemical input into the environment. Recently, Piriformospora indica, a plant-root-colonizing basidiomycete fungus, has been discovered in the Indian Thar desert and was shown to provide strong growth-promoting activity during its symbiosis with a broad spectrum of plants. Here, we report on the potential of P. indica to induce resistance to fungal diseases and tolerance to salt stress in the monocotyledonous plant barley. The beneficial effect on the defense status is detected in distal leaves, demonstrating a systemic induction of resistance by a root-endophytic fungus. The systemically altered "defense readiness" is associated with an elevated antioxidative capacity due to an activation of the glutathione-ascorbate cycle and results in an overall increase in grain yield. Because P. indica can be easily propagated in the absence of a host plant, we conclude that the fungus could be exploited to increase disease resistance and yield in crop plants.

Ascorbic Acid↗
PubMed2004

Identification of mycorrhiza-regulated genes with arbuscule development-related expression profile.

Suppressive subtractive hybridisation was applied to the analysis of late stage arbuscular mycorrhizal development in pea. 96 cDNA clones were amplified and 81, which carried fragments more than 200 nt in size, were sequence analysed. Among 67 unique fragments, 10 showed no homology and 10 were similar to sequences with unknown function. RNA accumulation of the corresponding 67 genes was analysed by hybridisation of macro-arrays. The cDNAs used as probes were derived from roots of wild type and late mutant pea genotypes, inoculated or not with the AM fungus Glomus mosseae. After calibration, a more than 2.5-fold mycorrhiza-induced RNA accumulation was detected in two independent experiments in the wild type for 25 genes, 22 of which seemed to be induced specifically during late stage AM development. Differential expression for 7 genes was confirmed by RT-PCR using RNA from mycorrhiza and from controls of a different pea cultivar. In order to confirm arbuscule-related expression, the Medicago truncatula EST data base was screened for homologous sequences with putative mycorrhiza-related expression and among a number of sequences with significant similarities, a family of trypsin inhibitor genes could be identified. Mycorrhiza-induced RNA accumulation was verified for five members by real-time PCR and arbuscule-related activation of the promoter could be shown in transgenic roots for one of the genes, MtTi 1.

Expressed Sequence Tags↗
PubMed2003

Transcriptional changes in response to arbuscular mycorrhiza development in the model plant Medicago truncatula.

Significant changes in root morphology and physiology during arbuscular mycorrhiza (AM) development are likely to be controlled by specific gene expression pattern in the host plant. Until now, little was known about transcriptional changes which occur AM-exclusively; that is, they do not occur during other root-microbe associations, nor are they induced by improved phosphate nutrition. In order to identify such AM-exclusive gene inductions of Medicago truncatula, we used a pool of different RNA samples as subtractor population in a suppressive subtractive hybridization (SSH) experiment. This approach resulted in the identification of a number of new AM-regulated genes. None of these genes were expressed in nonmycorrhiza roots or leaves. Electronic data obtained by comparison of the cDNA sequences to expressed sequence tag (EST) sequences from a wide range of cDNA libraries in the M. truncatula EST database (Gene Index, MtGI) support the mycorrhiza specificity of the corresponding genes, because sequences in the MtGI that were found to match the identified SSH-cDNA sequences originated exclusively from AM cDNA libraries. The promoter of one of those genes, MtGst1, showing similarities to plant glutathione-S-transferase (GST) encoding genes, was cloned and used in reporter gene studies. In contrast to studies with the potato GST gene PRP, MtGst 1 promoter activity was detected in all zones of the root cortex colonized by Glomus intraradices, but nowhere else.

Base Sequence↗
PubMed2003

Root factors induce mitochondrial-related gene expression and fungal respiration during the developmental switch from asymbiosis to presymbiosis in the arbuscular mycorrhizal fungus Gigaspora rosea.

During spore germination, arbuscular mycorrhizal (AM) fungi show limited hyphal development in the absence of a host plant (asymbiotic). In the presence of root exudates, they switch to a new developmental stage (presymbiotic) characterized by extensive hyphal branching. Presymbiotic branching of the AM fungus Gigaspora rosea was induced in liquid medium by a semipurified exudate fraction from carrot (Daucus carota) root organ cultures. Changes in RNA accumulation patterns were monitored by differential display analysis. Differentially appearing cDNA fragments were cloned and further analyzed. Five cDNA fragments could be identified that show induced RNA accumulation 1 h after the addition of root exudate. Sequence similarities of two fragments to mammalian Nco4 and mitochondrial rRNA genes suggested that root exudates could influence fungal respiratory activity. To support this hypothesis, additional putative mitochondrial related-genes were shown to be induced by root exudates. These genes were identified after subtractive hybridization and putatively encode a pyruvate carboxylase and a mitochondrial ADP/ATP translocase. The gene GrosPyc1 for the pyruvate carboxylase was studied in more detail by cloning a cDNA and by quantifying its RNA accumulation. The hypothesis that respiratory activity of AM fungi is stimulated by root exudates was confirmed by physiological and cytological analyses in G. rosea and Glomus intraradices. Oxygen consumption and reducing activity of both fungi was induced after 3 and 2 h of exposition with the root factor, respectively, and the first respiration activation was detected in G. intraradices after approximately 90 min. In addition, changes in mitochondrial morphology, orientation, and overall biomass were detected in G. rosea after 4 h. In summary, the root-exuded factor rapidly induces the expression of certain fungal genes and, in turn, fungal respiratory activity before intense branching. This defines the developmental switch from asymbiosis to presymbiosis, first by gene activation (0.5-1 h), subsequently on the physiological level (1.5-3 h), and finally as a morphological response (after 5 h).

Cell Respiration↗
PubMed2003

Symbiotic status, phosphate, and sucrose regulate the expression of two plasma membrane H+-ATPase genes from the mycorrhizal fungus Glomus mosseae.

The establishment of the arbuscular mycorrhizal symbiosis results in a modification of the gene expression pattern in both plant and fungus to accomplish the morphological and physiological changes necessary for the bidirectional transfer of nutrients between symbionts. H(+)-ATPase enzymes play a key role establishing the electrochemical gradient required for the transfer of nutrients across the plasma membrane in both fungi and plants. Molecular analysis of the genetic changes in arbuscular mycorrhizal fungi during symbiosis allowed us to isolate a fungal cDNA clone encoding a H(+)-ATPase, GmPMA1, from Glomus mosseae (BEG12). Despite the high conservation of the catalytic domain from H(+)-ATPases, detailed analyses showed that GmPMA1 was strongly related only to a previously identified G. mosseae ATPase gene, GmHA5, and not to the other four ATPase genes known from this fungus. A developmentally regulated expression pattern could be shown for both genes, GmPMA1 and GmHA5. GmPMA1 was highly expressed during asymbiotic development, and its expression did not change when entering into symbiosis, whereas the GmHA5 transcript was induced upon plant recognition at the appressorium stage. Both genes maintained high levels of expression during intraradical development, but their expression was reduced in the extraradical mycelium. Phosphate, a key nutrient to the symbiosis, also induced the expression of GmHA5 during asymbiotic growth, whereas sucrose had a negative effect. Our results indicate that different fungal H(+)-ATPases isoforms might be recruited at different developmental stages possibly responding to the different requirements of the life in symbiosis.

Amino Acid Sequence↗