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At least 19 recordsLinked to original sources
PubMed2005

Global patterns of gene regulation associated with the development of ectomycorrhiza between birch (Betula pendula Roth.) and Paxillus involutus (Batsch) Fr.

The formation of ectomycorrhizal (ECM) root tissue is characterized by distinct morphological and developmental stages, such as preinfection and adhesion, mantle, and Hartig net formation. The global pattern of gene expression during these stages in the birch (Betula pendula)-Paxillus involutus ECM association was analyzed using cDNA microarrays. In comparison with nonsymbiotic conditions, 251 fungal (from a total of 1,075) and 138 plant (1,074 in total) genes were found to be differentially regulated during the ECM development. For instance, during mantle and Hartig net development, there were several plant genes upregulated that are normally involved in defense responses during pathogenic fungal challenges. These responses were, at later stages of ECM development, found to be repressed. Other birch genes that showed differential regulation involved several homologs that usually are implicated in water permeability (aquaporins) and water stress tolerance (dehydrins). Among fungal genes differentially upregulated during stages of mantle and Hartig net formation were homologs putatively involved in mitochondrial respiration. In fully developed ECM tissue, there was an upregulation of fungal genes related to protein synthesis and the cytoskeleton assembly machinery. This study highlights complex molecular interactions between two symbionts during the development of an ECM association.

Base Sequence↗
PubMed1996

Transcriptional repression of specific host genes by the mycovirus Cryphonectria hypovirus 1.

The hypovirus CHV1, which infects the plant-pathogenic fungus Cryphonectria parasitica, causes a distinct range of symptoms in its host that include reduced virulence expression, reduced sporulation, and reduced pigmentation. The virus, however, has little or no effect on fungal growth in culture. The visual symptoms are associated with reduced accumulation of a small number of host mRNAs and proteins. Four of the host genes encoding these down-regulated mRNAs have been characterized; they include two genes encoding a fungal sex pheromone (Vir1 and Vir2), a gene encoding an extracellular laccase (Lac1), and a gene encoding a cell wall hydrophobin (Crp). Expression of most other host proteins appears to be unaffected by the virus. These four genes can serve as reporter genes in studies of the effect of the virus on host gene expression. It is hypothesized that the four genes are coordinately down-regulated by the virus and probably are associated in a regulatory cascade. This hypothesis was tested by measuring the relative transcription rate of each gene in virus-infected and uninfected isogenic strains of the fungus by using nuclear run-on assays. The effects of the virus on transcription of these genes generally mirrored the observed effects of the virus on relative accumulation of the mRNAs of each gene. Although repressed transcription cannot account for all of the effects of the virus on mRNA accumulation of these four reporter genes, it is the predominant effect.

Amanitins↗
PubMed2001

Differential regulation of gene expression in the obligate biotrophic interaction of Uromyces fabae with its host Vicia faba.

Classical analysis of obligate biotrophic fungi revealed changes of enzyme activities or the concentration of metabolites in infected areas. However, due to the intricate integration of host and parasite metabolism, it was not possible to delineate the individual contributions of the two organisms. Here, we used reverse-transcription-polymerase chain reaction to monitor expression of genes from the rust fungus Uromyces fabae and its host Vicia faba. We focused on genes relevant for amino acid and sugar uptake and metabolism in both organisms. In the fungus, mRNA for plasma membrane ATPase was detected in spores and all infection structures. Two genes for fungal amino acid transporters showed dissimilar regulation. Transcripts for one were detected during all developmental stages, whereas those of the other appeared to be under developmental control. The latter result was also obtained for the so far only hexose transporter known from U. fabae and for one gene of the thiamine biosynthesis pathway. In the host plant, transcripts for two ATPases analyzed generally declined upon infection. Sucrose synthase expression increased in leaves, but decreased in roots. Transcript levels of glucose and sucrose transporter genes appeared unchanged. Markers for amino acid metabolism did not show a uniform trend: transcripts for asparagine synthetase increased, whereas those for two amino acid transporters either decreased or increased. Our analyses revealed that not only expression of genes in the immediate vicinity of the primary infection site is altered, but infection also influences transcription of certain genes in remote organs, like stems and roots. This demonstrates alterations in the source-sink relationships.

Basidiomycota↗
PubMed1995

A temperature-sensitive lambda cI repressor functions on a modified operator in yeast cells by masking the TATA element.

We describe the construction and analysis of derivatives of the yeast TDH3 promoter in which the TATA box element has been replaced by a portion of the phage lambda operator containing a consensus TATA site flanked by binding sites for the cI repressor. Transcription of a reporter gene under the control of such a promoter is reduced in cells that express the cI repressor protein. Deletion of the native TATA element of the TDH3 promoter reduces transcription to the same extent. The cI repressor may act by "masking" the TATA element located between the repressor binding sites. Furthermore, the use of a temperature-sensitive cI repressor allowed temperature-dependent transcription of the reporter gene.

Bacteriophage lambda↗
PubMed2006

PIP aquaporin gene expression in arbuscular mycorrhizal Glycine max and Lactuca sativa plants in relation to drought stress tolerance.

Although the discovery of aquaporins in plants has resulted in a paradigm shift in the understanding of plant water relations, the relationship between aquaporins and plant responses to drought still remains elusive. Moreover, the contribution of aquaporin genes to the enhanced tolerance to drought in arbuscular mycorrhisal (AM) plants has never been investigated. Therefore, we studied, at a molecular level, whether the expression of aquaporin-encoding genes in roots is altered by the AM symbiosis as a mechanism to enhance host plant tolerance to water deficit. In this study, genes encoding plasma membrane aquaporins (PIPs) from soybean and lettuce were cloned and their expression pattern studied in AM and nonAM plants cultivated under well-watered or drought stressed conditions. Results showed that AM plants responded to drought stress by down-regulating the expression of the PIP genes studied and anticipating its down-regulation as compared to nonAM plants. The possible physiological implications of this down-regulation of PIP genes as a mechanism to decrease membrane water permeability and to allow cellular water conservation is further discussed.

Aquaporins↗
PubMed2000

The [KIL-d] element specifically regulates viral gene expression in yeast.

The cytoplasmically inherited [KIL-d] element epigenetically regulates killer virus gene expression in Saccharomyces cerevisiae. [KIL-d] results in variegated defects in expression of the M double-stranded RNA viral segment in haploid cells that are "healed" in diploids. We report that the [KIL-d] element is spontaneously lost with a frequency of 10(-4)-10(-5) and reappears with variegated phenotypic expression with a frequency of > or =10(-3). This high rate of loss and higher rate of reappearance is unlike any known nucleic acid replicon but resembles the behavior of yeast prions. However, [KIL-d] is distinct from the known yeast prions in its relative guanidinium hydrochloride incurability and independence of Hsp104 protein for its maintenance. Despite its transmissibility by successive cytoplasmic transfers, multiple cytoplasmic nucleic acids have been proven not to carry the [KIL-d] trait. [KIL-d] epigenetically regulates the expression of the M double-stranded RNA satellite virus genome, but fails to alter the expression of M cDNA. This specificity remained even after a cycle of mating and meiosis. Due to its unique genetic properties and viral RNA specificity, [KIL-d] represents a new type of genetic element that interacts with a viral RNA genome.

Base Sequence↗
PubMed2000

cDNA-AFLP display for the isolation of Peronospora parasitica genes expressed during infection in Arabidopsis thaliana.

To identify genes from the obligatory biotrophic oomycete Peronospora parasitica that are expressed during infection in Arabidopsis thaliana we employed cDNA-amplified fragment length polymorphism (AFLP) display. cDNA-AFLP fragments from infected and non-infected leaves were separated in parallel by gel electrophoresis and displayed by autoradiography. Most differential gene fragments were derived from P. parasitica.

Arabidopsis↗
PubMed1998

Co-expression of human eIF-4G and poliovirus 2Apro in Saccharomyces cerevisiae: effects on gene expression.

The poliovirus 5' untranslated region (5' UTR) confers on mRNAs the capacity to be translated by internal initiation. The functionality of this RNA motif has been tested in yeast cells (Saccharomyces cerevisiae) using luciferase (luc) as a reporter gene. Although some luciferase is synthesized from luc mRNA containing the poliovirus 5' UTR (Leader-luc mRNA), much more luciferase is synthesized in cells that express luc mRNA devoid of the poliovirus 5' UTR. Since poliovirus 2Apro enhances the translation of Leader-luc mRNAs after eIF-4G cleavage in mammalian cells, yeast cells were produced that synthesize three heterologous proteins, luciferase, poliovirus 2Apro and human eIF-4G. Initially, S. cerevisiae cells constitutively expressing human eIF-4G were isolated. The human eIF-4G gene does not complement yeast cells defective in the initiation factor counterpart, p150, indicating that the human and yeast eIF-4G are not interchangeable. Expression of poliovirus 2Apro in an inducible manner does not affect p150, but led to the efficient cleavage of human eIF-4G in yeast cells. Induction of 2Apro was detrimental to luciferase synthesis either from luc mRNA or Leader-luc mRNA irrespective of the presence or absence of human eIF-4G. 2Apro blocked luciferase expression at the transcriptional level. Finally, the effects of 16 point mutations of poliovirus 2Apro on luciferase expression and human eIF-4G cleavage were analysed. Only those 2Apro variants that generate viable polioviruses actively cleave eIF-4G in yeast.

Amino Acid Sequence↗
PubMed2003

Clustering gene expression data using adaptive double self-organizing map.

This paper presents a novel clustering technique known as adaptive double self-organizing map (ADSOM). ADSOM has a flexible topology and performs clustering and cluster visualization simultaneously, thereby requiring no a priori knowledge about the number of clusters. ADSOM is developed based on a recently introduced technique known as double self-organizing map (DSOM). DSOM combines features of the popular self-organizing map (SOM) with two-dimensional position vectors, which serve as a visualization tool to decide how many clusters are needed. Although DSOM addresses the problem of identifying unknown number of clusters, its free parameters are difficult to control to guarantee correct results and convergence. ADSOM updates its free parameters during training, and it allows convergence of its position vectors to a fairly consistent number of clusters provided that its initial number of nodes is greater than the expected number of clusters. The number of clusters can be identified by visually counting the clusters formed by the position vectors after training. A novel index is introduced based on hierarchical clustering of the final locations of position vectors. The index allows automated detection of the number of clusters, thereby reducing human error that could be incurred from counting clusters visually. The reliance of ADSOM in identifying the number of clusters is proven by applying it to publicly available gene expression data from multiple biological systems such as yeast, human, and mouse. ADSOM's performance in detecting number of clusters is compared with a model-based clustering method.

Animals↗
PubMed2005

GC-compositional strand bias around transcription start sites in plants and fungi.

BACKGROUND: A GC-compositional strand bias or GC-skew (=(C-G)/(C+G)), where C and G denote the numbers of cytosine and guanine residues, was recently reported near the transcription start sites (TSS) of Arabidopsis genes. However, it is unclear whether other eukaryotic species have equally prominent GC-skews, and the biological meaning of this trait remains unknown. RESULTS: Our study confirmed a significant GC-skew (C > G) in the TSS of Oryza sativa (rice) genes. The full-length cDNAs and genomic sequences from Arabidopsis and rice were compared using statistical analyses. Despite marked differences in the G+C content around the TSS in the two plants, the degrees of bias were almost identical. Although slight GC-skew peaks, including opposite skews (C < G), were detected around the TSS of genes in human and Drosophila, they were qualitatively and quantitatively different from those identified in plants. However, plant-like GC-skew in regions upstream of the translation initiation sites (TIS) in some fungi was identified following analyses of the expressed sequence tags and/or genomic sequences from other species. On the basis of our dataset, we estimated that > 70 and 68% of Arabidopsis and rice genes, respectively, had a strong GC-skew (> 0.33) in a 100-bp window (that is, the number of C residues was more than double the number of G residues in a +/-100-bp window around the TSS). The mean GC-skew value in the TSS of highly-expressed genes in Arabidopsis was significantly greater than that of genes with low expression levels. Many of the GC-skew peaks were preferentially located near the TSS, so we examined the potential value of GC-skew as an index for TSS identification. Our results confirm that the GC-skew can be used to assist the TSS prediction in plant genomes. CONCLUSION: The GC-skew (C > G) around the TSS is strictly conserved between monocot and eudicot plants (ie. angiosperms in general), and a similar skew has been observed in some fungi. Highly-expressed Arabidopsis genes had overall a more marked GC-skew in the TSS compared to genes with low expression levels. We therefore propose that the GC-skew around the TSS in some plants and fungi is related to transcription. It might be caused by mutations during transcription initiation or the frequent use of transcription factor-biding sites having a strand preference. In addition, GC-skew is a good candidate index for TSS prediction in plant genomes, where there is a lack of correlation among CpG islands and genes.

Arabidopsis↗
PubMed2004

TXTGate: profiling gene groups with text-based information.

We implemented a framework called TXTGate that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes. By means of tailored vocabularies, term- as well as gene-centric views are offered on selected textual fields and MEDLINE abstracts used in LocusLink and the Saccharomyces Genome Database. Subclustering and links to external resources allow for in-depth analysis of the resulting term profiles.

Animals↗
PubMed1996

Repeat-induced gene silencing: common mechanisms in plants and fungi.

One of the most surprising observations made in plant science in recent years is the inactivation of transgenes triggered by interactions between DNA repeats. In plants, we can differentiate between transcriptional silencing, most likely reflecting a regulation at the DNA level, and post-transcriptional silencing that affects steady state RNA levels. In the filamentous fungi Ascobolus immersus and Neurospora crassa, we find two premeiotic silencing processes that are also based on the interaction of repeated sequences. A common feature of transcriptional silencing in plants and premeiotic gene inactivation in filamentous fungi is that the repeated sequences undergo cytosine methylation. DNA methylation, which is either the cause or the consequence of gene silencing, can be associated with changes in chromatin structure. These structural changes are reminiscent of homology-based silencing mechanisms in Drosophila, an organism that lacks DNA methylation. Repeat-induced silencing may therefore reflect the activity of an endogenous mechanism, present in some species, which screens for homology and has significant implications for the organization and evolution of the genome.

Gene Expression Regulation, Fungal↗
PubMed2003

Expression profiling of up-regulated plant and fungal genes in early and late stages of Medicago truncatula-Glomus mosseae interactions.

Suppression subtractive hybridization (SSH), expression profiling and EST sequencing identified 12 plant genes and six fungal genes that are expressed in the arbuscular mycorrhizal symbiosis between Medicago truncatula and Glomus mosseae. All the plant genes and three of the fungal genes were up-regulated in symbiotic tissues. Expression of 15 of the genes is described for the first time in mycorrhizal roots and two are novel sequences. Six M. truncatula genes were also activated during appressorium formation at the root surface, suggesting a role in this early stage of mycorrhiza establishment, whilst the other six plant genes were only induced in the late stages of mycorrhization and could be involved in the development or functioning of the symbiosis. Phosphate fertilization had no significant influence on expression of any of the plant genes. Expression profiling of G. mosseae genes indicated that two of them may be associated with appressorium development on roots and one with arbuscule formation or function. The other three fungal genes were expressed throughout the life-cycle of G. mosseae.

DNA, Complementary↗
PubMed2001

A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae.

The relationship between the similarity of expression patterns for a pair of genes and interaction of the proteins they encode is demonstrated both for the simple genome of the bacteriophage T7 and the considerably more complex genome of the yeast Saccharomyces cerevisiae. Statistical analysis of large-scale gene expression and protein interaction data shows that protein pairs encoded by co-expressed genes interact with each other more frequently than with random proteins. Furthermore, the mean similarity of expression profiles is significantly higher for respective interacting protein pairs than for random ones. Such coupled analysis of gene expression and protein interaction data may allow evaluation of the results of large-scale gene expression and protein interaction screens as demonstrated for several publicly available datasets. The role of this link between expression and interaction in the evolution from monomeric to oligomeric protein structures is also discussed.

Bacteriophage T7↗
PubMed1993

Histones, nucleosomes and transcription.

It is becoming increasingly clear that nucleosome structure is integrally involved in gene regulation. In particular, the study of inducible genes has shown that nucleosomes not only contribute to a repressed basal state, but can also be rearranged in response to induction. The mechanism of this process is just beginning to be elucidated, and genetic studies have implicated several proteins in the modulation of nucleosome structure.

Animals↗
PubMed2006

Fungal and plant gene expression in arbuscular mycorrhizal symbiosis.

Arbuscular mycorrhizas (AMs) are a unique example of symbiosis between two eukaryotes, soil fungi and plants. This association induces important physiological changes in each partner that lead to reciprocal benefits, mainly in nutrient supply. The symbiosis results from modifications in plant and fungal cell organization caused by specific changes in gene expression. Recently, much effort has gone into studying these gene expression patterns to identify a wider spectrum of genes involved. We aim in this review to describe AM symbiosis in terms of current knowledge on plant and fungal gene expression profiles.

Gene Expression Regulation, Fungal↗
PubMed1997

A peroxidase gene promoter induced by phytopathogens and methyl jasmonate in transgenic plants.

The expression of two closely related peroxidase isogenes, Shpx6a and Shpx6b, of the legume Stylosanthes humilis was studied using isogene-specific reverse transcriptase PCR techniques. Results indicated that transcripts of both genes were rapidly induced following inoculation with the fungal pathogen Colletotrichum gloeosporioides, wounding and treatment with the defense regulator methyl jasmonate (MeJA). In contrast treatment of leaves of S. humilis with abscisic acid (ABA) and salicylic acid (SA) did not induce transcripts of either isogene. A genomic clone containing the Shpx6b gene was isolated and 594 bp of 5' sequence upstream of the translation start was fused in frame to the coding region of the uidA reporter gene and introduced into tobacco. Expression from the Shpx6b promoter in transgenic plants was determined by histochemical staining and quantitative assays of beta-glucuronidase (GUS). In transgenic tobacco, GUS expression was detected in cotyledons, vascular cells of young leaves, anthers, pollen, and the stigma and style. Wounding of the tobacco plants produced very localized GUS staining. Much more extensive staining for GUS was observed following inoculation of tobacco leaves with conidia of the fungal pathogen Cercospora nicotianae and the inoculation of wound sites with mycelium of the Oomycete pathogen Phytophthora parasitica var. nicotianae. Treatment of mature leaves with methyl jasmonate induced GUS activity while treatment with ABA, SA, and H2O2 had no effect. A similar strong induction of GUS activity was measured in young transgenic seedlings germinated on MeJA while some, but much weaker, induction of GUS activity was observed in seedlings treated with SA. The sequence of the promoter contained motifs homologous to putative cis elements in other plant genes responsive to MeJA. The Shpx6b gene is the first plant peroxidase gene shown to be induced by both microbial pathogens and MeJA and its promoter will be useful for investigations of signaling processes during fungal infection and for the expression of foreign gene products at infection sites.

Acetates↗
PubMed2005

Transcript patterns associated with ectomycorrhiza development in Eucalyptus globulus and Pisolithus microcarpus.

Regulated gene expression is an important mechanism for controlling ectomycorrhizal symbiosis development. This study aimed to elucidate the coordination between development of mycorrhiza and the differential gene expression in both partners. We analysed RNA levels from sequential samples of symbiotic tissues of Eucalyptus globulus bicostata and the basidiomycete Pisolithus microcarpus progressing through ectomycorrhiza development using cDNA arrays. We derived groups of coordinately expressed genes using hierarchical and nonhierarchical clustering algorithms. Five major distinct temporal patterns of induction/repression were observed with distinct groups of early, middle-, and late-transcriptionally responsive genes to symbiosis formation. At earliest stages, the differentially expressed fungal genes included cell wall symbiosis-regulated proteins, hydrophobins and mannoproteins, whereas transcripts coding for defense-related proteins were upregulated in plant tissues. Middle- and late-transcriptionally responsive genes coded enzymes of glycolysis, tricarboxylic acid cycle and amino acid biosynthesis, as well as protein synthesis, hormone metabolism and signal transduction components. This investigation confirms and extends earlier results which found that changes in morphology associated with mycorrhizal development were accompanied by changes in transcript patterns, but no ectomycorrhiza-specific genes were detected.

Basidiomycota↗