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Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia.

Santana PB, Junior RG, Alves CN, Silva JL, McCulloch JA, Schneider MP, da Costa da Silva A - Genet. Mol. Biol. (2012)

Bottom Line: Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane.The 3D structures of the archaean Mcrα observed in the present study varied little, and presented approximately 70% identity in comparison with the Mcrα of Methanopyrus klanderi.The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.

ABSTRACT
Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane. Using a metagenomic approach, the gene of the α subunit of mcr (mcrα) was isolated from sediment sample from an anoxic zone, rich in decomposing organic material, obtained from the Tucuruí hydroelectric dam reservoir in eastern Brazilian Amazonia. The partial nucleotide sequences obtained were 83 to 95% similar to those available in databases, indicating a low diversity of archaeans in the reservoir. Two orders were identified - the Methanomicrobiales, and a unique Operational Taxonomic Unit (OTU) forming a clade with the Methanosarcinales according to low bootstrap values. Homology modeling was used to determine the three-dimensional (3D) structures, for this the partial nucleotide sequence of the mcrα were isolated and translated on their partial amino acid sequences. The 3D structures of the archaean Mcrα observed in the present study varied little, and presented approximately 70% identity in comparison with the Mcrα of Methanopyrus klanderi. The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.

No MeSH data available.


Multiple alignment of the amino acid sequences of the Mcrα of Methanospyrus klandery, showing the template and the sequences obtained in the present study using the Clustal 2.0.9 program: Tuc14 and Tuc18 (clade 1), Tuc21 and Tuc22 (clade 2), and Tuc10 and Tuc1 (clade 3). Residuals identical to the sequence template are marked with an asterisk, and those that differ between the template and the target are marked with dots. The bars represent the degree of conservation of the respective residual.
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f4-gmb-35-1-126: Multiple alignment of the amino acid sequences of the Mcrα of Methanospyrus klandery, showing the template and the sequences obtained in the present study using the Clustal 2.0.9 program: Tuc14 and Tuc18 (clade 1), Tuc21 and Tuc22 (clade 2), and Tuc10 and Tuc1 (clade 3). Residuals identical to the sequence template are marked with an asterisk, and those that differ between the template and the target are marked with dots. The bars represent the degree of conservation of the respective residual.

Mentions: Clades 1 and 2 of the gene trees showed higher homology level with the Mcrα of M. klanderi. Figure 4 clearly shows their close similarity by the multiple alignment of target sequences, clades 1 and 2, and the template sequence, M. klanderi. Clade 3 and Tuc29 showed higher homology level with the Mcrα of M. barkery.


Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia.

Santana PB, Junior RG, Alves CN, Silva JL, McCulloch JA, Schneider MP, da Costa da Silva A - Genet. Mol. Biol. (2012)

Multiple alignment of the amino acid sequences of the Mcrα of Methanospyrus klandery, showing the template and the sequences obtained in the present study using the Clustal 2.0.9 program: Tuc14 and Tuc18 (clade 1), Tuc21 and Tuc22 (clade 2), and Tuc10 and Tuc1 (clade 3). Residuals identical to the sequence template are marked with an asterisk, and those that differ between the template and the target are marked with dots. The bars represent the degree of conservation of the respective residual.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3313501&req=5

f4-gmb-35-1-126: Multiple alignment of the amino acid sequences of the Mcrα of Methanospyrus klandery, showing the template and the sequences obtained in the present study using the Clustal 2.0.9 program: Tuc14 and Tuc18 (clade 1), Tuc21 and Tuc22 (clade 2), and Tuc10 and Tuc1 (clade 3). Residuals identical to the sequence template are marked with an asterisk, and those that differ between the template and the target are marked with dots. The bars represent the degree of conservation of the respective residual.
Mentions: Clades 1 and 2 of the gene trees showed higher homology level with the Mcrα of M. klanderi. Figure 4 clearly shows their close similarity by the multiple alignment of target sequences, clades 1 and 2, and the template sequence, M. klanderi. Clade 3 and Tuc29 showed higher homology level with the Mcrα of M. barkery.

Bottom Line: Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane.The 3D structures of the archaean Mcrα observed in the present study varied little, and presented approximately 70% identity in comparison with the Mcrα of Methanopyrus klanderi.The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.

ABSTRACT
Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane. Using a metagenomic approach, the gene of the α subunit of mcr (mcrα) was isolated from sediment sample from an anoxic zone, rich in decomposing organic material, obtained from the Tucuruí hydroelectric dam reservoir in eastern Brazilian Amazonia. The partial nucleotide sequences obtained were 83 to 95% similar to those available in databases, indicating a low diversity of archaeans in the reservoir. Two orders were identified - the Methanomicrobiales, and a unique Operational Taxonomic Unit (OTU) forming a clade with the Methanosarcinales according to low bootstrap values. Homology modeling was used to determine the three-dimensional (3D) structures, for this the partial nucleotide sequence of the mcrα were isolated and translated on their partial amino acid sequences. The 3D structures of the archaean Mcrα observed in the present study varied little, and presented approximately 70% identity in comparison with the Mcrα of Methanopyrus klanderi. The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.

No MeSH data available.