Transcriptome analysis by cDNA-AFLP of Suillus luteus Cd-tolerant and Cd-sensitive isolates

Ruytinx, Joske; Craciun, Adrian Radu; Verstraelen, Karen; Vangronsveld, Jaco; Colpaert, Jan; Verbruggen, Nathalie

doi:10.1007/s00572-010-0318-2

Cited by 23 publications

(23 citation statements)

References 45 publications

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“…And it is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. Since the invention of this method has found widespread use as an attractive technology for gene discovery on the basis of fragment detection and for temporal quantitative gene expression analysis, such as, rice [5], wheat [6], Arabidopsis [7], bean [8], and you can process a number of important physiological and biochemical characteristics of gene expression system [9].…”

Section: Introductionmentioning

confidence: 99%

Notice of Retraction: Optimization of cDNA-aFLP Amplification Reaction System in Strawberry Leaves

Miao

Zhang

Yang

et al. 2011

2011 5th International Conference on Bioinformatics and Biomedical Engineering

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In this study in order to uncover the mechanism of strawberry inoculated with colletotrichum gloeosporioides and isolation the related genes, an optimized cDNA-AFLP procedure was established. The cDNA-AFLP procedures including RNA extraction, mRNA isolation reverse transcription, enzyme digestion, pre-amplification, selective amplification, silver staining. The factors affecting cDNA-AFLP analysis system with young leaves of strawberry in this study were optimized. According to the optimized reaction system, the polymorphous strips in 6% PAGE electrophoresis were clear and stable and the cDNA-AFLP reaction system developed and optimized in this experiment provided valuable information for further molecular biology and gene cloning studies on strawberry.

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Section: Introductionmentioning

confidence: 99%

Notice of Retraction: Optimization of cDNA-aFLP Amplification Reaction System in Strawberry Leaves

Miao

Zhang

Yang

et al. 2011

2011 5th International Conference on Bioinformatics and Biomedical Engineering

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“…Interestingly, for each gene, the level of expression that was induced by nickel varied among the isolates tested. This intraspecific variation in transcript profiles was also observed in cadmium‐tolerant Suillus luteus isolates, which suggests that such variation helps fungal species to persist in novel environments (Ruytinx et al. 2011).…”

Section: Discussionmentioning

confidence: 75%

“…Additional mechanisms include antioxidative responses (Muller et al. 2007a; Ruytinx et al. 2011), extracellular chelation and binding of the metal to the cell wall (Bellion et al.…”

Section: Introductionmentioning

confidence: 99%

Tracking nickel‐adaptive biomarkers in Pisolithus albus from New Caledonia using a transcriptomic approach

et al. 2012

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The fungus Pisolithus albus forms ectomycorrhizal (ECM) associations with plants growing on extreme ultramafic soils, which are naturally rich in heavy metals such as nickel. Both nickel-tolerant and nickel-sensitive isolates of P. albus are found in ultramafic soils in New Caledonia, a biodiversity hotspot in the Southwest Pacific. The aim of this work was to monitor the expression of genes involved in the specific molecular response to nickel in a nickel-tolerant P. albus isolate. We used pyrosequencing and quantitative polymerase chain reaction (qPCR) approaches to investigate and compare the transcriptomes of the nickel-tolerant isolate MD06-337 in the presence and absence of nickel. A total of 1,071,375 sequencing reads were assembled to infer expression patterns of 19,518 putative genes. Comparison of expression levels revealed that 30% of the identified genes were modulated by nickel treatment. The genes, for which expression was induced most markedly by nickel, encoded products that were putatively involved in a variety of biological functions, such as the modification of cellular components (53%), regulation of biological processes (27%) and molecular functions (20%). The 10 genes that pyrosequencing analysis indicated were induced the most by nickel were characterized further by qPCR analysis of both nickel-tolerant and nickel-sensitive P. albus isolates. Five of these genes were expressed exclusively in nickel-tolerant isolates as well as in ECM samples in situ, which identified them as potential biomarkers for nickel tolerance in this species. These results clearly suggest a positive transcriptomic response of the fungus to nickel-rich environments. The presence of both nickel-tolerant and nickel-sensitive fungal phenotypes in ultramafic soils might reflect environment-dependent phenotypic responses to variations in the effective concentrations of nickel in heterogeneous ultramafic habitats.

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“…All primer sequences are provided in the Supporting information (Table S4) with JGI protein ID or GenBank accession number deposited previously (Ruytinx et al, 2011). Gene expression was calculated relative to the sample with the highest expression (relative expression 5 2 -(Cq(sample)-Cq(min) ), normalized to four reference genes using a normalization factor (geometric mean of relative expression levels of the reference genes, Vandesompele et al, 2002) and rescaled to the non-exposed control (fold changes).…”

Section: Cloning Of Slmta and Slmtb Genesmentioning

confidence: 99%

“…It has been reported to occur at various metal polluted sites in Europe (Colpaert et al ., ; Op De Beeck et al ., ). Some mechanisms of metal tolerance in this fungus have been studied before (Colpaert et al ., ; Ruytinx et al ., ) but metal chelation via MTs has not yet been reported. In this study, we identified and functionally characterized two novel MT coding genes of S. luteus and searched for their homologs in other basidiomycete genomes.…”

Section: Introductionmentioning

confidence: 99%

A novel, highly conserved metallothionein family in basidiomycete fungi and characterization of two representative SlMTa and SlMTb genes in the ectomycorrhizal fungus Suillus luteus

Nguyen

Rineau

Vangronsveld

et al. 2017

Environmental Microbiology

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The basidiomycete Suillus luteus is an important member of the ectomycorrhizal community that thrives in heavy metal polluted soils covered with pioneer pine forests. This study aimed to identify potential heavy metal chelators in S. luteus. Two metallothionein (MT) coding genes, SlMTa and SlMTb, were identified. When heterologously expressed in yeast, both SlMTa and SlMTb can rescue the Cu sensitive mutant from Cu toxicity. In S. luteus, transcription of both SlMTa and SlMTb is induced by Cu but not Cd or Zn. Several putative Cu-sensing and metal-response elements are present in the promoter sequences. These results indicate that SlMTa and SlMTb function as Cu-thioneins. Homologs of the S. luteus MTs are present in 49 species belonging to 10 different orders of the subphylum Agaricomycotina and are remarkably conserved. The length of the proteins, number and distribution of cysteine residues indicate a novel family of fungal MTs. The ubiquitous and highly conserved features of these MTs suggest that they are important for basic cellular functions in species in the subphylum Agaricomycotina.

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Transcriptome analysis by cDNA-AFLP of Suillus luteus Cd-tolerant and Cd-sensitive isolates

Cited by 23 publications

References 45 publications

Notice of Retraction: Optimization of cDNA-aFLP Amplification Reaction System in Strawberry Leaves

Notice of Retraction: Optimization of cDNA-aFLP Amplification Reaction System in Strawberry Leaves

Tracking nickel‐adaptive biomarkers in Pisolithus albus from New Caledonia using a transcriptomic approach

A novel, highly conserved metallothionein family in basidiomycete fungi and characterization of two representative SlMTa and SlMTb genes in the ectomycorrhizal fungus Suillus luteus

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