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Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily.

Muratore KE, Engelhardt BE, Srouji JR, Jordan MI, Brenner SE, Kirsch JF - Proteins (2013)

Bottom Line: The enzymes that were experimentally characterized include both narrow-specificity AATases and broad-specificity TATases, as well as AATases with broader-specificity and TATases with narrower-specificity than the previously known family members.Molecular function and phylogenetic analyses underscored the complexity of this family's evolution as the TATase function does not follow a single evolutionary thread, but rather appears independently multiple times during the evolution of the subfamily.The additional functional characterizations described in this article, alongside a detailed sequence and phylogenetic analysis, provide some novel clues to understanding the evolutionary mechanisms at work in this family.

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Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California.

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Groups of diverse aminotransferases. The choice of enzymes that were characterized (indicated by asterisks) and the grouping into similar sets by the D&V method are described in Materials and Methods. Identification numbers refer to Swiss-Prot entry names or UniProt accession numbers38 (UniProt accession numbers for Swiss-Prot sequences are provided in Supporting Information Table S1). The abbreviations used throughout this manuscript are as follows: AtcAT: AAT4_ARATH (Arabidopsis thaliana cytosolic); AtmAT: AAT1_ARATH (A. thaliana mitochondrial); CecAT: AATC_CAEEL (C. elegans cytosolic); CtAT: O84642 (Chlamydia trachomatis); GicAT: Q964E9 (Giardia intestinalis cytosolic); PfcAT: O96142 (Plasmodium falciparum cytosolic); ScmAT: AATM_YEAST (Saccharomyces cerevisiae mitochondrial); TbcAT: Q964F1 (Trypanosoma brucei cytosolic); TbmAT: Q964E0 (T. brucei mitochondrial); VcAT: Q9KM75 (Vibrio cholerae).
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fig02: Groups of diverse aminotransferases. The choice of enzymes that were characterized (indicated by asterisks) and the grouping into similar sets by the D&V method are described in Materials and Methods. Identification numbers refer to Swiss-Prot entry names or UniProt accession numbers38 (UniProt accession numbers for Swiss-Prot sequences are provided in Supporting Information Table S1). The abbreviations used throughout this manuscript are as follows: AtcAT: AAT4_ARATH (Arabidopsis thaliana cytosolic); AtmAT: AAT1_ARATH (A. thaliana mitochondrial); CecAT: AATC_CAEEL (C. elegans cytosolic); CtAT: O84642 (Chlamydia trachomatis); GicAT: Q964E9 (Giardia intestinalis cytosolic); PfcAT: O96142 (Plasmodium falciparum cytosolic); ScmAT: AATM_YEAST (Saccharomyces cerevisiae mitochondrial); TbcAT: Q964F1 (Trypanosoma brucei cytosolic); TbmAT: Q964E0 (T. brucei mitochondrial); VcAT: Q9KM75 (Vibrio cholerae).

Mentions: For each position chosen using the D&V criteria, a sequence's score (the D&V score) increased by one for each residue that was different from the corresponding residues in all the 10 characterized reference sequences in the given alignment. The total possible D&V score was 76, based on the total number of chosen residues in these sequences. Most of the sequences were similar or identical to those that had been previously characterized and consequently had D&V scores of 10 or less. A smaller set of thirty-two sequences with a D&V score > 10, and, therefore, greater sequence diversity near the active site, were carried forward for further analysis. A pair-wise score was calculated for each of these 32 top-scoring sequences to create a distance matrix in order to group the sequences according to their relative divergence. To compute the pair-wise score, two sequences were compared at each position that contributed to the original D&V score in that sequence, and one was added to the pair-wise score for each residue that was mismatched between the two sequences. These pair-wise scores are not necessarily symmetric since the positions contributing to the original D&V score may be different for each sequence. Pairs of sequences where both members of the pair score <9 relative to each other were placed into the same group (Fig. 2). One enzyme from each of these 10 groups was chosen for characterization based on gene availability. Thus, the active site of each enzyme that was selected was different from the 10 original reference enzymes, and also different from each of the other nine newly selected enzymes.


Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily.

Muratore KE, Engelhardt BE, Srouji JR, Jordan MI, Brenner SE, Kirsch JF - Proteins (2013)

Groups of diverse aminotransferases. The choice of enzymes that were characterized (indicated by asterisks) and the grouping into similar sets by the D&V method are described in Materials and Methods. Identification numbers refer to Swiss-Prot entry names or UniProt accession numbers38 (UniProt accession numbers for Swiss-Prot sequences are provided in Supporting Information Table S1). The abbreviations used throughout this manuscript are as follows: AtcAT: AAT4_ARATH (Arabidopsis thaliana cytosolic); AtmAT: AAT1_ARATH (A. thaliana mitochondrial); CecAT: AATC_CAEEL (C. elegans cytosolic); CtAT: O84642 (Chlamydia trachomatis); GicAT: Q964E9 (Giardia intestinalis cytosolic); PfcAT: O96142 (Plasmodium falciparum cytosolic); ScmAT: AATM_YEAST (Saccharomyces cerevisiae mitochondrial); TbcAT: Q964F1 (Trypanosoma brucei cytosolic); TbmAT: Q964E0 (T. brucei mitochondrial); VcAT: Q9KM75 (Vibrio cholerae).
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3823064&req=5

fig02: Groups of diverse aminotransferases. The choice of enzymes that were characterized (indicated by asterisks) and the grouping into similar sets by the D&V method are described in Materials and Methods. Identification numbers refer to Swiss-Prot entry names or UniProt accession numbers38 (UniProt accession numbers for Swiss-Prot sequences are provided in Supporting Information Table S1). The abbreviations used throughout this manuscript are as follows: AtcAT: AAT4_ARATH (Arabidopsis thaliana cytosolic); AtmAT: AAT1_ARATH (A. thaliana mitochondrial); CecAT: AATC_CAEEL (C. elegans cytosolic); CtAT: O84642 (Chlamydia trachomatis); GicAT: Q964E9 (Giardia intestinalis cytosolic); PfcAT: O96142 (Plasmodium falciparum cytosolic); ScmAT: AATM_YEAST (Saccharomyces cerevisiae mitochondrial); TbcAT: Q964F1 (Trypanosoma brucei cytosolic); TbmAT: Q964E0 (T. brucei mitochondrial); VcAT: Q9KM75 (Vibrio cholerae).
Mentions: For each position chosen using the D&V criteria, a sequence's score (the D&V score) increased by one for each residue that was different from the corresponding residues in all the 10 characterized reference sequences in the given alignment. The total possible D&V score was 76, based on the total number of chosen residues in these sequences. Most of the sequences were similar or identical to those that had been previously characterized and consequently had D&V scores of 10 or less. A smaller set of thirty-two sequences with a D&V score > 10, and, therefore, greater sequence diversity near the active site, were carried forward for further analysis. A pair-wise score was calculated for each of these 32 top-scoring sequences to create a distance matrix in order to group the sequences according to their relative divergence. To compute the pair-wise score, two sequences were compared at each position that contributed to the original D&V score in that sequence, and one was added to the pair-wise score for each residue that was mismatched between the two sequences. These pair-wise scores are not necessarily symmetric since the positions contributing to the original D&V score may be different for each sequence. Pairs of sequences where both members of the pair score <9 relative to each other were placed into the same group (Fig. 2). One enzyme from each of these 10 groups was chosen for characterization based on gene availability. Thus, the active site of each enzyme that was selected was different from the 10 original reference enzymes, and also different from each of the other nine newly selected enzymes.

Bottom Line: The enzymes that were experimentally characterized include both narrow-specificity AATases and broad-specificity TATases, as well as AATases with broader-specificity and TATases with narrower-specificity than the previously known family members.Molecular function and phylogenetic analyses underscored the complexity of this family's evolution as the TATase function does not follow a single evolutionary thread, but rather appears independently multiple times during the evolution of the subfamily.The additional functional characterizations described in this article, alongside a detailed sequence and phylogenetic analysis, provide some novel clues to understanding the evolutionary mechanisms at work in this family.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California.

Show MeSH
Related in: MedlinePlus