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Comparative molecular evolution of trichoderma chitinases in response to mycoparasitic interactions.

Ihrmark K, Asmail N, Ubhayasekera W, Melin P, Stenlid J, Karlsson M - Evol. Bioinform. Online (2010)

Bottom Line: Two of them, chi18-13 and chi18-17, are members of the B1/B2 chitinase subgroup that have expanded significantly in paralog number in mycoparasitic Hypocrea atroviridis and H. virens.Differences in amino acid diversity/conservation patterns between different Trichoderma clades are observed.These observations show that Trichoderma chitinases chi18-13 and chi18-15 evolve in a manner consistent with rapid co-evolutionary interactions and identifies putative target regions involved in determining substrate-specificity.

View Article: PubMed Central - PubMed

Affiliation: Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, S-75007, Uppsala, Sweden.

ABSTRACT
Certain species of the fungal genus Trichoderma are potent mycoparasites and are used for biological control of fungal diseases on agricultural crops. In Trichoderma, whole-genome sequencing reveal between 20 and 36 different genes encoding chitinases, hydrolytic enzymes that are involved in the mycoparasitic attack. Sequences of Trichoderma chitinase genes chi18-5, chi18-13, chi18-15 and chi18-17, which all exhibit specific expression during mycoparasitism-related conditions, were determined from up to 13 different taxa and studied with regard to their evolutionary patterns. Two of them, chi18-13 and chi18-17, are members of the B1/B2 chitinase subgroup that have expanded significantly in paralog number in mycoparasitic Hypocrea atroviridis and H. virens. Chi18-13 contains two codons that evolve under positive selection and seven groups of co-evolving sites. Chi18-15 displays a unique codon-usage and contains five codons that evolve under positive selection and three groups of co-evolving sites. Regions of high amino acid variability are preferentially localized to substrate- or product side of the catalytic clefts. Differences in amino acid diversity/conservation patterns between different Trichoderma clades are observed. These observations show that Trichoderma chitinases chi18-13 and chi18-15 evolve in a manner consistent with rapid co-evolutionary interactions and identifies putative target regions involved in determining substrate-specificity.

No MeSH data available.


Related in: MedlinePlus

Reverse conservation analysis of chi18-5 orthologs. Amino acid diversity was estimated using Rate4Site, based on a Clustal X alignment of chi18-5 Trichoderma orthologs, and plotted as W mean scores. The y-axis represents arbitrary units (not shown) while a horizontal line indicates a 0.5 standard deviation cutoff. The x-axis represents residue position, asterisks (*) indicate positions of catalytic residues, diamonds (⋄) indicate substrate-interacting residues. The positions of the signal peptide and regions with high amino acid diversity successfully visualised by homology modelling are indicated (Ia–VIIa).
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f1-ebo-2010-001: Reverse conservation analysis of chi18-5 orthologs. Amino acid diversity was estimated using Rate4Site, based on a Clustal X alignment of chi18-5 Trichoderma orthologs, and plotted as W mean scores. The y-axis represents arbitrary units (not shown) while a horizontal line indicates a 0.5 standard deviation cutoff. The x-axis represents residue position, asterisks (*) indicate positions of catalytic residues, diamonds (⋄) indicate substrate-interacting residues. The positions of the signal peptide and regions with high amino acid diversity successfully visualised by homology modelling are indicated (Ia–VIIa).

Mentions: Amplification products and full-length sequences for chi18-5 orthologs were successfully obtained from H. schweinitzii, T. ghanense and T. longibrachiatum. Additional sequences from H. jecorina, H. atroviridis and H. virens were retrieved from genome sequences and used for RCA analysis. A unique insert of 18 bp in H. virens chi18-5 was excluded from the analysis. A phylogenetic analysis confirmed the orthologous status of the sequenced genes (Supplemental Figure S3). Amino acid diversity was distributed amongst eight regions with W mean scores above the 0.5 standard deviation threshold from the RCA analysis (Fig. 1). One of these regions was associated with the signal peptide cleavage site, while the other seven regions (Ia, IIa, IIIa, IVa, Va, VIa and VIIa) were visualized (Fig. 2A) using a homology model of H. jecorina chi18-5. Several of the twenty predicted residues (Supplemental Table S2) important for catalysis and substrate binding (cd06548 in Conserved Domain Database (CDD)56) were located in conserved regions with low W scores (Fig. 1). Three residues were located in regions with high W mean scores, one each in IIa, IIIa and IVa (Fig. 2A). These three regions, IIa, IIIa and IVa, were all surface-exposed and located on the product side of the enzyme. Region Ia was located in a loop that forms the entrance to the catalytic cleft, while region VIIa is on the surface of the enzyme but far from the catalytic site (Fig. 2A).


Comparative molecular evolution of trichoderma chitinases in response to mycoparasitic interactions.

Ihrmark K, Asmail N, Ubhayasekera W, Melin P, Stenlid J, Karlsson M - Evol. Bioinform. Online (2010)

Reverse conservation analysis of chi18-5 orthologs. Amino acid diversity was estimated using Rate4Site, based on a Clustal X alignment of chi18-5 Trichoderma orthologs, and plotted as W mean scores. The y-axis represents arbitrary units (not shown) while a horizontal line indicates a 0.5 standard deviation cutoff. The x-axis represents residue position, asterisks (*) indicate positions of catalytic residues, diamonds (⋄) indicate substrate-interacting residues. The positions of the signal peptide and regions with high amino acid diversity successfully visualised by homology modelling are indicated (Ia–VIIa).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2865166&req=5

f1-ebo-2010-001: Reverse conservation analysis of chi18-5 orthologs. Amino acid diversity was estimated using Rate4Site, based on a Clustal X alignment of chi18-5 Trichoderma orthologs, and plotted as W mean scores. The y-axis represents arbitrary units (not shown) while a horizontal line indicates a 0.5 standard deviation cutoff. The x-axis represents residue position, asterisks (*) indicate positions of catalytic residues, diamonds (⋄) indicate substrate-interacting residues. The positions of the signal peptide and regions with high amino acid diversity successfully visualised by homology modelling are indicated (Ia–VIIa).
Mentions: Amplification products and full-length sequences for chi18-5 orthologs were successfully obtained from H. schweinitzii, T. ghanense and T. longibrachiatum. Additional sequences from H. jecorina, H. atroviridis and H. virens were retrieved from genome sequences and used for RCA analysis. A unique insert of 18 bp in H. virens chi18-5 was excluded from the analysis. A phylogenetic analysis confirmed the orthologous status of the sequenced genes (Supplemental Figure S3). Amino acid diversity was distributed amongst eight regions with W mean scores above the 0.5 standard deviation threshold from the RCA analysis (Fig. 1). One of these regions was associated with the signal peptide cleavage site, while the other seven regions (Ia, IIa, IIIa, IVa, Va, VIa and VIIa) were visualized (Fig. 2A) using a homology model of H. jecorina chi18-5. Several of the twenty predicted residues (Supplemental Table S2) important for catalysis and substrate binding (cd06548 in Conserved Domain Database (CDD)56) were located in conserved regions with low W scores (Fig. 1). Three residues were located in regions with high W mean scores, one each in IIa, IIIa and IVa (Fig. 2A). These three regions, IIa, IIIa and IVa, were all surface-exposed and located on the product side of the enzyme. Region Ia was located in a loop that forms the entrance to the catalytic cleft, while region VIIa is on the surface of the enzyme but far from the catalytic site (Fig. 2A).

Bottom Line: Two of them, chi18-13 and chi18-17, are members of the B1/B2 chitinase subgroup that have expanded significantly in paralog number in mycoparasitic Hypocrea atroviridis and H. virens.Differences in amino acid diversity/conservation patterns between different Trichoderma clades are observed.These observations show that Trichoderma chitinases chi18-13 and chi18-15 evolve in a manner consistent with rapid co-evolutionary interactions and identifies putative target regions involved in determining substrate-specificity.

View Article: PubMed Central - PubMed

Affiliation: Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, S-75007, Uppsala, Sweden.

ABSTRACT
Certain species of the fungal genus Trichoderma are potent mycoparasites and are used for biological control of fungal diseases on agricultural crops. In Trichoderma, whole-genome sequencing reveal between 20 and 36 different genes encoding chitinases, hydrolytic enzymes that are involved in the mycoparasitic attack. Sequences of Trichoderma chitinase genes chi18-5, chi18-13, chi18-15 and chi18-17, which all exhibit specific expression during mycoparasitism-related conditions, were determined from up to 13 different taxa and studied with regard to their evolutionary patterns. Two of them, chi18-13 and chi18-17, are members of the B1/B2 chitinase subgroup that have expanded significantly in paralog number in mycoparasitic Hypocrea atroviridis and H. virens. Chi18-13 contains two codons that evolve under positive selection and seven groups of co-evolving sites. Chi18-15 displays a unique codon-usage and contains five codons that evolve under positive selection and three groups of co-evolving sites. Regions of high amino acid variability are preferentially localized to substrate- or product side of the catalytic clefts. Differences in amino acid diversity/conservation patterns between different Trichoderma clades are observed. These observations show that Trichoderma chitinases chi18-13 and chi18-15 evolve in a manner consistent with rapid co-evolutionary interactions and identifies putative target regions involved in determining substrate-specificity.

No MeSH data available.


Related in: MedlinePlus