Open Access Research article

The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold

Francisco J Fernandez1*, Fernando Garces2, Miguel López-Estepa1, Juan Aguilar3, Laura Baldomà3, Miquel Coll45, Josefa Badia3 and M Cristina Vega1*

Author Affiliations

1 Structural and Quantitative Biology Department, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain

2 Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK

3 Departament de Bioquímica i Biologia Molecular, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Spain

4 Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain

5 Institute for Research in Biomedicine (IRB Barcelona), Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain

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BMC Evolutionary Biology 2011, 11:273  doi:10.1186/1471-2148-11-273

Published: 26 September 2011

Additional files

Additional file 1:

Figure S1. Genetic organization and transcriptional direction of the utilization of L-ascorbate (ula) regulon in Escherichia coli and encoded structural genes.

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Additional file 2:

Figure S2. Catabolism of L-ascorbate 6-phosphate in enterobacteria and established catalytic activity of E. coli UlaG.

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Additional file 3:

Table S1. Sequences included in the phylogenetic analyses.

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Additional file 4:

Bacterial UlaGL sequences. FASTA file containing the complete set of bacterial UlaGL sequences.

Format: FASTA Size: 88KB Download file

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Additional file 5:

Filtered multiple sequence alignment of bacterial UlaGL sequences. Multiple sequence alignment of bacterial UlaGL sequences in FASTA format prior to Gblocks filtering.

Format: FASTA Size: 78KB Download file

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Additional file 6:

Unfiltered multiple sequence alignment of bacterial UlaGL sequences. Multiple sequence alignment of bacterial UlaGL sequences in FASTA format after Gblocks filtering, used for phylogenetic reconstruction.

Format: FASTA Size: 70KB Download file

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Additional file 7:

Phylogenetic tree of bacterial UlaGL. Majority rule consensus tree of bacterial UlaGL sequences calculated with MrBayes and RAxML (used to prepare Figure 3). Nodes are labeled with BIPP (Bayesian inference posterior probability) and MLBP (maximum-likelihood bootstrap percentage).

Format: TREE Size: 61KB Download file

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Additional file 8:

Gammaproteobacterial species tree used for comparison with UlaGL tree. Phylogenetic tree constructed from a set of representative Gammaproteobacteria species that encode UlaGL, used for the evaluation of potential HGT events between related gammaproteobacterial species. Internal nodes are labeled with maximum-likelihood branch length support (MLBL). Tree was calculated with Tree-Puzzle v. 5.2

Format: TREE Size: 4KB Download file

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Additional file 9:

Archeal UlaGL sequences. FASTA file containing the set of archeal UlaGL sequences.

Format: FASTA Size: 7KB Download file

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Additional file 10:

Unfiltered multiple sequence alignment of archeal UlaGL sequences. Multiple sequence alignment of archeal UlaGL sequences in FASTA format prior to Gblocks filtering.

Format: FASTA Size: 9KB Download file

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Additional file 11:

Filtered multiple sequence alignment of archeal UlaGL sequences. Multiple sequence alignment of archeal UlaGL sequences in FASTA format after Gblocks filtering, used for phylogenetic reconstruction.

Format: FASTA Size: 5KB Download file

Open Data

Additional file 12:

Phylogenetic tree of archeal UlaGL. Majority rule consensus tree of archeal UlaGL sequences (using two eubacterial sequences as outgroups) calculated with MrBayes and RAxML (used to prepare Figure 5). Nodes are labeled with BIPP (Bayesian inference posterior probability) and MLBP (maximum-likelihood bootstrap percentage).

Format: TREE Size: 5KB Download file

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Additional file 13:

Table S2. Homology modeling, interfaces, and geometry validation of UlaGL homology models generated with MODELLER-9v8.

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Additional file 14:

Table S3. Analysis of buried contact area by PISA of reference structures and homology models generated with MODELLER-9v8.

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