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Xenomic networks variability and adaptation traits in wood decaying fungi.

Morel M, Meux E, Mathieu Y, Thuillier A, Chibani K, Harvengt L, Jacquot JP, Gelhaye E - Microb Biotechnol (2013)

Bottom Line: Taking advantage of the recent release of numerous genomes of basidiomycetes, we show here that these multigenic families are extended and functionally related in wood-decaying fungi.Furthermore, we postulate that these rapidly evolving multigenic families could reflect the adaptation of these fungi to the diversity of their substrate and provide keys to understand their ecology.This is of particular importance for white biotechnology, this xenome being a putative target for improving degradation properties of these fungi in biomass valorization purposes.

View Article: PubMed Central - PubMed

Affiliation: Université de Lorraine, IAM, UMR 1136, IFR 110 EFABA, Vandoeuvre-lès-Nancy, F-54506, France. mmorel@scbiol.uhp-nancy.fr

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Related in: MedlinePlus

Phylogenetic tree of glutathione transferases from Basidiomycetes. Various subclasses could be distinguished: Ure2p, GSTFuA, Omega (GSTO), Glutathionyl Hydroquinone Reductase (GHR), Phi, GTT1 and GTT2. The sequences were retrieved from genomes available on the Joint Genome Institute (http://www.jgi.doe.gov/). Sequence alignments were done by clustalw and the tree was constructed with the neighbour-joining method in MEGA 5.0 software (Tamura et al., 2011). The robustness of the branches was assessed by the bootstrap method with 500 replications. The scale marker represents 0.2 substitutions per residue.
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fig02: Phylogenetic tree of glutathione transferases from Basidiomycetes. Various subclasses could be distinguished: Ure2p, GSTFuA, Omega (GSTO), Glutathionyl Hydroquinone Reductase (GHR), Phi, GTT1 and GTT2. The sequences were retrieved from genomes available on the Joint Genome Institute (http://www.jgi.doe.gov/). Sequence alignments were done by clustalw and the tree was constructed with the neighbour-joining method in MEGA 5.0 software (Tamura et al., 2011). The robustness of the branches was assessed by the bootstrap method with 500 replications. The scale marker represents 0.2 substitutions per residue.

Mentions: Soluble GSTs are usually dimeric enzymes, each monomer being composed of two domains. The N-terminal domain, which is more or less conserved, is involved in glutathione binding (G-site). The C-terminal domain is more variable and is involved in the binding of substrates (H-site). The nomenclature of cytosolic GSTs is based on amino acid sequence identity and at least eight classes have been described to date in fungi and named GTT1, GTT2, URE2p, MAK16, EFb1, Etherase-like recently renamed GSTFuA (Mathieu et al., 2012), GSTO and GHR (McGoldrick et al., 2005, Morel et al., 2009) (Fig. 2). Traditionally, two proteins belong to the same class if they share more than 40% identity and isoenzymes belonging to different classes share less than 20% (Hayes et al., 2005). Nevertheless, based on these primary sequence criteria only, many ‘non-canonical’ GST groups have emerged especially in bacteria and fungi, increasing the complexity of the GSTs classification. A few protein families are usually classified as GSTs (EF1Bγ, MAK16), but this is rather based on structural similarities, not on the existence of a glutathione-dependent activity. In addition, further immunologic, genetic, structural and functional investigations could reveal unexpected similarities between enzymes first listed in different groups (Meux et al., 2012). This emphasizes the challenge of GST classification.


Xenomic networks variability and adaptation traits in wood decaying fungi.

Morel M, Meux E, Mathieu Y, Thuillier A, Chibani K, Harvengt L, Jacquot JP, Gelhaye E - Microb Biotechnol (2013)

Phylogenetic tree of glutathione transferases from Basidiomycetes. Various subclasses could be distinguished: Ure2p, GSTFuA, Omega (GSTO), Glutathionyl Hydroquinone Reductase (GHR), Phi, GTT1 and GTT2. The sequences were retrieved from genomes available on the Joint Genome Institute (http://www.jgi.doe.gov/). Sequence alignments were done by clustalw and the tree was constructed with the neighbour-joining method in MEGA 5.0 software (Tamura et al., 2011). The robustness of the branches was assessed by the bootstrap method with 500 replications. The scale marker represents 0.2 substitutions per residue.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815920&req=5

fig02: Phylogenetic tree of glutathione transferases from Basidiomycetes. Various subclasses could be distinguished: Ure2p, GSTFuA, Omega (GSTO), Glutathionyl Hydroquinone Reductase (GHR), Phi, GTT1 and GTT2. The sequences were retrieved from genomes available on the Joint Genome Institute (http://www.jgi.doe.gov/). Sequence alignments were done by clustalw and the tree was constructed with the neighbour-joining method in MEGA 5.0 software (Tamura et al., 2011). The robustness of the branches was assessed by the bootstrap method with 500 replications. The scale marker represents 0.2 substitutions per residue.
Mentions: Soluble GSTs are usually dimeric enzymes, each monomer being composed of two domains. The N-terminal domain, which is more or less conserved, is involved in glutathione binding (G-site). The C-terminal domain is more variable and is involved in the binding of substrates (H-site). The nomenclature of cytosolic GSTs is based on amino acid sequence identity and at least eight classes have been described to date in fungi and named GTT1, GTT2, URE2p, MAK16, EFb1, Etherase-like recently renamed GSTFuA (Mathieu et al., 2012), GSTO and GHR (McGoldrick et al., 2005, Morel et al., 2009) (Fig. 2). Traditionally, two proteins belong to the same class if they share more than 40% identity and isoenzymes belonging to different classes share less than 20% (Hayes et al., 2005). Nevertheless, based on these primary sequence criteria only, many ‘non-canonical’ GST groups have emerged especially in bacteria and fungi, increasing the complexity of the GSTs classification. A few protein families are usually classified as GSTs (EF1Bγ, MAK16), but this is rather based on structural similarities, not on the existence of a glutathione-dependent activity. In addition, further immunologic, genetic, structural and functional investigations could reveal unexpected similarities between enzymes first listed in different groups (Meux et al., 2012). This emphasizes the challenge of GST classification.

Bottom Line: Taking advantage of the recent release of numerous genomes of basidiomycetes, we show here that these multigenic families are extended and functionally related in wood-decaying fungi.Furthermore, we postulate that these rapidly evolving multigenic families could reflect the adaptation of these fungi to the diversity of their substrate and provide keys to understand their ecology.This is of particular importance for white biotechnology, this xenome being a putative target for improving degradation properties of these fungi in biomass valorization purposes.

View Article: PubMed Central - PubMed

Affiliation: Université de Lorraine, IAM, UMR 1136, IFR 110 EFABA, Vandoeuvre-lès-Nancy, F-54506, France. mmorel@scbiol.uhp-nancy.fr

Show MeSH
Related in: MedlinePlus