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Successful conversion of the Bacillus subtilis BirA Group II biotin protein ligase into a Group I ligase.

Henke SK, Cronan JE - PLoS ONE (2014)

Bottom Line: The Bacillus subtilis BPL, BirA, is classified as a Group II BPL based on sequence predictions of an N-terminal helix-turn-helix motif and mutational alteration of its regulatory properties.Moreover, unlike the paradigm Group II BPL, E. coli BirA, the N-terminal DNA binding domain can be deleted from Bacillus subtilis BirA without adverse effects on its ligase function.This is the first example of successful conversion of a Group II BPL to a Group I BPL with retention of full ligase activity.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America.

ABSTRACT
Group II biotin protein ligases (BPLs) are characterized by the presence of an N-terminal DNA binding domain that allows transcriptional regulation of biotin biosynthetic and transport genes whereas Group I BPLs lack this N-terminal domain. The Bacillus subtilis BPL, BirA, is classified as a Group II BPL based on sequence predictions of an N-terminal helix-turn-helix motif and mutational alteration of its regulatory properties. We report evidence that B. subtilis BirA is a Group II BPL that regulates transcription at three genomic sites: bioWAFDBI, yuiG and yhfUTS. Moreover, unlike the paradigm Group II BPL, E. coli BirA, the N-terminal DNA binding domain can be deleted from Bacillus subtilis BirA without adverse effects on its ligase function. This is the first example of successful conversion of a Group II BPL to a Group I BPL with retention of full ligase activity.

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Sequence alignments of S. aureus BPL, B. subtilis BirA and E. coli BirA.B. subtilis BirA has 31% amino acid identity to S. aureus BPL and 27% amino acid identity to E. coli BirA. Conserved residues are in white text and highlighted in red and similar residues are in red text and boxed in blue. The S. aureus BPL secondary structure (PDB: 4DQ2) is shown above the amino acid sequence.
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pone-0096757-g002: Sequence alignments of S. aureus BPL, B. subtilis BirA and E. coli BirA.B. subtilis BirA has 31% amino acid identity to S. aureus BPL and 27% amino acid identity to E. coli BirA. Conserved residues are in white text and highlighted in red and similar residues are in red text and boxed in blue. The S. aureus BPL secondary structure (PDB: 4DQ2) is shown above the amino acid sequence.

Mentions: The sequences of other Group II BPLs suggest such proteins are found in γ-Proteobacteria, Bacilli, and Clostridii [2], although only the proteins from E. coli[6] and (very recently) Staphylococcus aureus[7] have been enzymatically characterized and crystallized. One of the Group II BPLs, B. subtilis BirA, has only 27% amino acid sequence identity to E. coli BirA (Fig. 2). Despite this low sequence identity, Bacillus subtilis birA has been shown to complement the ligase activity of a temperature-sensitive E. coli birA85 strain [18]. Moreover, B. subtilis birA mutants show constitutive expression of a bioW-lacZ fusion, suggesting that BirA regulates biotin operon transcription [18]. B. subtilis microarray data identified two additional transcripts, yuiG and yhfUST, regulated by biotin and BirA [19]. Both YuiG and YhfU have strong sequence similarity to the structurally characterized BioY biotin transporter of Lactococcus lactis[20] and other well characterized energy-coupling factor (ECF) biotin transporters [21]. All three transcripts have similar predicted BirA binding sites [2], [19]. B. subtilis has two known biotinylated proteins, pyruvate carboxylase (PyC) and the biotin carboxyl carrier protein (AccB) subunit of acetyl-CoA carboxylase (http://genodb.pasteur.fr). A third B. subtilis protein, biotin/lipoyl attachment protein (BLAP) encoded by the yngHB gene was found to be biotinylated and lipoylated when expressed in E. coli[22] although subsequently this protein was found not to be lipoylated by the B. subtilis enzymes that modify the known cognate lipoic acid acceptor proteins [23].


Successful conversion of the Bacillus subtilis BirA Group II biotin protein ligase into a Group I ligase.

Henke SK, Cronan JE - PLoS ONE (2014)

Sequence alignments of S. aureus BPL, B. subtilis BirA and E. coli BirA.B. subtilis BirA has 31% amino acid identity to S. aureus BPL and 27% amino acid identity to E. coli BirA. Conserved residues are in white text and highlighted in red and similar residues are in red text and boxed in blue. The S. aureus BPL secondary structure (PDB: 4DQ2) is shown above the amino acid sequence.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4016012&req=5

pone-0096757-g002: Sequence alignments of S. aureus BPL, B. subtilis BirA and E. coli BirA.B. subtilis BirA has 31% amino acid identity to S. aureus BPL and 27% amino acid identity to E. coli BirA. Conserved residues are in white text and highlighted in red and similar residues are in red text and boxed in blue. The S. aureus BPL secondary structure (PDB: 4DQ2) is shown above the amino acid sequence.
Mentions: The sequences of other Group II BPLs suggest such proteins are found in γ-Proteobacteria, Bacilli, and Clostridii [2], although only the proteins from E. coli[6] and (very recently) Staphylococcus aureus[7] have been enzymatically characterized and crystallized. One of the Group II BPLs, B. subtilis BirA, has only 27% amino acid sequence identity to E. coli BirA (Fig. 2). Despite this low sequence identity, Bacillus subtilis birA has been shown to complement the ligase activity of a temperature-sensitive E. coli birA85 strain [18]. Moreover, B. subtilis birA mutants show constitutive expression of a bioW-lacZ fusion, suggesting that BirA regulates biotin operon transcription [18]. B. subtilis microarray data identified two additional transcripts, yuiG and yhfUST, regulated by biotin and BirA [19]. Both YuiG and YhfU have strong sequence similarity to the structurally characterized BioY biotin transporter of Lactococcus lactis[20] and other well characterized energy-coupling factor (ECF) biotin transporters [21]. All three transcripts have similar predicted BirA binding sites [2], [19]. B. subtilis has two known biotinylated proteins, pyruvate carboxylase (PyC) and the biotin carboxyl carrier protein (AccB) subunit of acetyl-CoA carboxylase (http://genodb.pasteur.fr). A third B. subtilis protein, biotin/lipoyl attachment protein (BLAP) encoded by the yngHB gene was found to be biotinylated and lipoylated when expressed in E. coli[22] although subsequently this protein was found not to be lipoylated by the B. subtilis enzymes that modify the known cognate lipoic acid acceptor proteins [23].

Bottom Line: The Bacillus subtilis BPL, BirA, is classified as a Group II BPL based on sequence predictions of an N-terminal helix-turn-helix motif and mutational alteration of its regulatory properties.Moreover, unlike the paradigm Group II BPL, E. coli BirA, the N-terminal DNA binding domain can be deleted from Bacillus subtilis BirA without adverse effects on its ligase function.This is the first example of successful conversion of a Group II BPL to a Group I BPL with retention of full ligase activity.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America.

ABSTRACT
Group II biotin protein ligases (BPLs) are characterized by the presence of an N-terminal DNA binding domain that allows transcriptional regulation of biotin biosynthetic and transport genes whereas Group I BPLs lack this N-terminal domain. The Bacillus subtilis BPL, BirA, is classified as a Group II BPL based on sequence predictions of an N-terminal helix-turn-helix motif and mutational alteration of its regulatory properties. We report evidence that B. subtilis BirA is a Group II BPL that regulates transcription at three genomic sites: bioWAFDBI, yuiG and yhfUTS. Moreover, unlike the paradigm Group II BPL, E. coli BirA, the N-terminal DNA binding domain can be deleted from Bacillus subtilis BirA without adverse effects on its ligase function. This is the first example of successful conversion of a Group II BPL to a Group I BPL with retention of full ligase activity.

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