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Diederik van Tuinen

Publications and source records attributed to Diederik van Tuinen.

4 recordsLinked to original sources

Molecular changes in Pisum sativum L. roots during arbuscular mycorrhiza buffering of cadmium stress.

Molecular responses to cadmium (Cd) stress were studied in mycorrhizal and non-mycorrhizal Pisum sativum L. cv. Frisson inoculated with Glomus intraradices. Biomass decreases caused by the heavy metal were significantly less in mycorrhizal than in non-mycorrhizal plants. Real-time reverse transcriptase-polymerase chain reaction showed that genes implicated in pathways of Cd detoxification varied in response to mycorrhiza development or Cd application. Expression of a metallothionein-encoding gene increased strongly in roots of Cd-treated non-mycorrhizal plants. Genes encoding gamma-glutamylcysteine synthetase and glutathione (GSH) synthetase, responsible for the synthesis of the phytochelatin (PC) precursor GSH, were activated by Cd in mycorrhizal and non-mycorrhizal plants. Cd stress decreased accumulation of GSH/homoglutathione (hGSH) and increased thiol groups in pea roots, whether mycorrhizal or not, suggesting synthesis of PCs and/or homophytochelatins. An hGSH synthetase gene, involved in hGSH synthesis, did not respond to Cd alone but was activated by mycorrhizal development in the presence of Cd. Transcript levels of a glutathione reductase gene were only increased in non-mycorrhizal roots treated with Cd. Studies of three stress-related genes showed that a heat-shock protein gene was activated in mycorrhizal roots or by Cd and chitinase gene transcripts increased under Cd stress to a greater extent in mycorrhizal roots, whilst a chalcone isomerase gene was only up-regulated by Cd. Results indicate that although heavy metal chelation pathways contribute to Cd stress responses in pea, they may not make a major contribution to Cd tolerance strategies operating in the arbuscular mycorrhizal symbiosis.

Adaptation, Physiological↗

Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula.

To construct macro- and microarray tools suitable for expression profiling in root endosymbioses of the model legume Medicago truncatula, we PCR-amplified a total of 6048 cDNA probes representing genes expressed in uninfected roots, mycorrhizal roots and young root nodules [Nucleic Acids Res. 30 (2002) 5579]. Including additional probes for either tissue-specific or constitutively expressed control genes, 5651 successfully amplified gene-specific probes were used to grid macro- and to spot microarrays designated Mt6k-RIT (M. truncatula 6k root interaction transcriptome). Subsequent to a technical validation of microarray printing, we performed two pilot expression profiling experiments using Cy-labeled targets from Sinorhizobium meliloti-induced root nodules and Glomus intraradices-colonized arbuscular mycorrhizal roots. These targets detected marker genes for nodule and arbuscular mycorrhiza development, amongst them different nodule-specific leghemoglobin and nodulin genes as well as a mycorrhiza-specific phosphate transporter gene. In addition, we identified several dozens of genes that have so far not been reported to be differentially expressed in nodules or arbuscular mycorrhiza thus demonstrating that Mt6k-RIT arrays serve as useful tools for an identification of genes relevant for legume root endosymbioses. A comprehensive profiling of such candidate genes will be very helpful to the development of breeding strategies and for the improvement of cultivation management targeted at increasing legume use in sustainable agricultural systems.

Equipment Design↗

Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis.

We report on a large-scale expressed sequence tag (EST) sequencing and analysis program aimed at characterizing the sets of genes expressed in roots of the model legume Medicago truncatula during interactions with either of two microsymbionts, the nitrogen-fixing bacterium Sinorhizobium meliloti or the arbuscular mycorrhizal fungus Glomus intraradices. We have designed specific tools for in silico analysis of EST data, in relation to chimeric cDNA detection, EST clustering, encoded protein prediction, and detection of differential expression. Our 21 473 5'- and 3'-ESTs could be grouped into 6359 EST clusters, corresponding to distinct virtual genes, along with 52 498 other M.truncatula ESTs available in the dbEST (NCBI) database that were recruited in the process. These clusters were manually annotated, using a specifically developed annotation interface. Analysis of EST cluster distribution in various M.truncatula cDNA libraries, supported by a refined R test to evaluate statistical significance and by 'electronic northern' representation, enabled us to identify a large number of novel genes predicted to be up- or down-regulated during either symbiotic root interaction. These in silico analyses provide a first global view of the genetic programs for root symbioses in M.truncatula. A searchable database has been built and can be accessed through a public interface.

Cluster Analysis↗

Repetitive DNA sequences include retrotransposons in genomes of the Glomeromycota.

Twenty-five repetitive elements are first described in the genomes of the arbuscular mycorrhizal (AM) fungi Gigaspora margarita, Gig. rosea and Glomus mosseae. Nineteen repetitive DNA sequences isolated by genomic library screening and four by self-priming PCR had no homology to known DNA sequences, except for two Gig. margarita sequences and one Gig. rosea sequence which showed amino acid similarity to retrotransposons. Part of the Gig. rosea sequence was also similar to a DNA transposon. Two other retrotransposon sequences were isolated using PCR targeting of reverse transcriptase and ribonuclease H domains. Evidence is provided for three gypsy-like LTR retrotransposon and two non-LTR retrotransposon sequences in the AM fungal genomes. Four contain stop codons indicating that they cannot be active. Expression of three retrotransposons was not detected in germinating spores or intraradical hyphae of Gig. margarita. Southern blot analyses indicated that these three sequences are dispersed in the genome and that two are methylated. Sequence analysis of different GmarLTR1 copies showed they have undergone mutations by transitions, which may have been induced by cytosine methylation. Transposable elements may have played a major role in shaping genome structure and size during evolution of the Glomeromycota.

Base Sequence↗