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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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The 3D structure of the RNA polymerase from the M. perniciosa mitochondrial plasmid. Magenta: helices; yellow: strands; blue: turn.
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Figure 3: The 3D structure of the RNA polymerase from the M. perniciosa mitochondrial plasmid. Magenta: helices; yellow: strands; blue: turn.

Mentions: The active site of the RNA polymerase (Figure 3) from M. perniciosa plasmid is formed by amino acids from two domains: Palm (Asp457 and Asp695) and Fingers (Tyr537 and Lys529) (Figure 4). In comparison to the template structure, these amino acids perform an alignment in the region of the active site, with the amino acids Asp537 and Asp812 (Palm), and Tyr639 and Lys631 (Fingers) of the template. The presence of these residues (Asp, Tyr, and Lys) in this region is a sign in this group of polymerases that they are involved with transcriptional processes [10,32,33].


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)

The 3D structure of the RNA polymerase from the M. perniciosa mitochondrial plasmid. Magenta: helices; yellow: strands; blue: turn.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: The 3D structure of the RNA polymerase from the M. perniciosa mitochondrial plasmid. Magenta: helices; yellow: strands; blue: turn.
Mentions: The active site of the RNA polymerase (Figure 3) from M. perniciosa plasmid is formed by amino acids from two domains: Palm (Asp457 and Asp695) and Fingers (Tyr537 and Lys529) (Figure 4). In comparison to the template structure, these amino acids perform an alignment in the region of the active site, with the amino acids Asp537 and Asp812 (Palm), and Tyr639 and Lys631 (Fingers) of the template. The presence of these residues (Asp, Tyr, and Lys) in this region is a sign in this group of polymerases that they are involved with transcriptional processes [10,32,33].

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