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Comparative modeling of DNA and RNA polymerases from Moniliophthora perniciosa mitochondrial plasmid.

Andrade BS, Taranto AG, Góes-Neto A, Duarte AA - Theor Biol Med Model (2009)

Bottom Line: This disease has resulted in a severe decrease in Brazilian cocoa production, which changed the position of Brazil in the market from the second largest cocoa exporter to a cocoa importer.MD simulations in water showed models with thermodynamic stability after 2000 ps and 300 K of simulation.This work contributes to the development of new alternatives for controlling the fungal agent of witches' broom disease.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil. bandradefsa@yahoo.com.br

ABSTRACT

Background: The filamentous fungus Moniliophthora perniciosa (Stahel) Aime & Phillips-Mora is a hemibiotrophic Basidiomycota that causes witches' broom disease of cocoa (Theobroma cacao L.). This disease has resulted in a severe decrease in Brazilian cocoa production, which changed the position of Brazil in the market from the second largest cocoa exporter to a cocoa importer. Fungal mitochondrial plasmids are usually invertrons encoding DNA and RNA polymerases. Plasmid insertions into host mitochondrial genomes are probably associated with modifications in host generation time, which can be involved in fungal aging. This association suggests activity of polymerases, and these can be used as new targets for drugs against mitochondrial activity of fungi, more specifically against witches' broom disease. Sequencing and modeling: DNA and RNA polymerases of M. perniciosa mitochondrial plasmid were completely sequenced and their models were carried out by Comparative Homology approach. The sequences of DNA and RNA polymerase showed 25% of identity to 1XHX and 1ARO (pdb code) using BLASTp, which were used as templates. The models were constructed using Swiss PDB-Viewer and refined with a set of Molecular Mechanics (MM) and Molecular Dynamics (MD) in water carried out with AMBER 8.0, both working under the ff99 force fields, respectively. Ramachandran plots were generated by Procheck 3.0 and exhibited models with 97% and 98% for DNA and RNA polymerases, respectively. MD simulations in water showed models with thermodynamic stability after 2000 ps and 300 K of simulation.

Conclusion: This work contributes to the development of new alternatives for controlling the fungal agent of witches' broom disease.

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ANOLEA validation of the built model. A) DPO; B) RPO. Green and red mean negative and positive values of energy.
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Figure 5: ANOLEA validation of the built model. A) DPO; B) RPO. Green and red mean negative and positive values of energy.

Mentions: Both the DNA and RNA polymerases, after refinement by optimization of geometry and MD simulations, had their structures validated by PROCHECK and ANOLEA (Figure 5). The Ramachandran plot showed that 97% and 98% of residues are within the allowed regions for DPO and RPO, respectively. Almost all residues show negative values of energy (green), whereas few amino acids obtained positive values of energy (red). This means that most residues are in a favourable energy environment. In other words, the quality of both main chain and side chain was evaluated showing that the models had appropriate stereochemical and thermodynamic values. As a result, although the target and template proteins showed a low homology identity, the tertiary structure obtained had the same sign of family.


Comparative modeling of DNA and RNA polymerases from Moniliophthora perniciosa mitochondrial plasmid.

Andrade BS, Taranto AG, Góes-Neto A, Duarte AA - Theor Biol Med Model (2009)

ANOLEA validation of the built model. A) DPO; B) RPO. Green and red mean negative and positive values of energy.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2746187&req=5

Figure 5: ANOLEA validation of the built model. A) DPO; B) RPO. Green and red mean negative and positive values of energy.
Mentions: Both the DNA and RNA polymerases, after refinement by optimization of geometry and MD simulations, had their structures validated by PROCHECK and ANOLEA (Figure 5). The Ramachandran plot showed that 97% and 98% of residues are within the allowed regions for DPO and RPO, respectively. Almost all residues show negative values of energy (green), whereas few amino acids obtained positive values of energy (red). This means that most residues are in a favourable energy environment. In other words, the quality of both main chain and side chain was evaluated showing that the models had appropriate stereochemical and thermodynamic values. As a result, although the target and template proteins showed a low homology identity, the tertiary structure obtained had the same sign of family.

Bottom Line: This disease has resulted in a severe decrease in Brazilian cocoa production, which changed the position of Brazil in the market from the second largest cocoa exporter to a cocoa importer.MD simulations in water showed models with thermodynamic stability after 2000 ps and 300 K of simulation.This work contributes to the development of new alternatives for controlling the fungal agent of witches' broom disease.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil. bandradefsa@yahoo.com.br

ABSTRACT

Background: The filamentous fungus Moniliophthora perniciosa (Stahel) Aime & Phillips-Mora is a hemibiotrophic Basidiomycota that causes witches' broom disease of cocoa (Theobroma cacao L.). This disease has resulted in a severe decrease in Brazilian cocoa production, which changed the position of Brazil in the market from the second largest cocoa exporter to a cocoa importer. Fungal mitochondrial plasmids are usually invertrons encoding DNA and RNA polymerases. Plasmid insertions into host mitochondrial genomes are probably associated with modifications in host generation time, which can be involved in fungal aging. This association suggests activity of polymerases, and these can be used as new targets for drugs against mitochondrial activity of fungi, more specifically against witches' broom disease. Sequencing and modeling: DNA and RNA polymerases of M. perniciosa mitochondrial plasmid were completely sequenced and their models were carried out by Comparative Homology approach. The sequences of DNA and RNA polymerase showed 25% of identity to 1XHX and 1ARO (pdb code) using BLASTp, which were used as templates. The models were constructed using Swiss PDB-Viewer and refined with a set of Molecular Mechanics (MM) and Molecular Dynamics (MD) in water carried out with AMBER 8.0, both working under the ff99 force fields, respectively. Ramachandran plots were generated by Procheck 3.0 and exhibited models with 97% and 98% for DNA and RNA polymerases, respectively. MD simulations in water showed models with thermodynamic stability after 2000 ps and 300 K of simulation.

Conclusion: This work contributes to the development of new alternatives for controlling the fungal agent of witches' broom disease.

Show MeSH