Structural characterization of <i>Staphylococcus aureus</i> biotin protein ligase and interaction partners: An antibiotic target

Pendini, Nicole R.; Yap, Min; Polyak, Steven W.; Cowieson, Nathan; Abell, Andrew D.; Booker, Grant W.; Wallace, John C.; Wilce, Jacqueline Anne; Wilce, Matthew C. J.

doi:10.1002/pro.2262

Cited by 35 publications

(59 citation statements)

References 55 publications

(64 reference statements)

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“…The BirA dimer binds to 40 base pairs of DNA and detailed chemical and DNase I footprints are consistent with a structure of the complex in which each monomer contacts approximately 12 base pairs at each terminus of the operator sequence with the center lacking any protein contacts [30]. The recently published SAXS-derived structure of the complex of Staphylococcus aureus holoBirA bound to its operator confirms this model [16]. Both the center of the operator sequence and the segments that contact each of the DNA binding domains undergo distortion upon binding to holoBirA.…”

Section: Discussionsupporting

confidence: 61%

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Protein:Protein Interactions in Control of a Transcriptional Switch

Adikaram

Beckett

2013

Journal of Molecular Biology

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Protein partner exchange plays a key role in regulating many biological switches. Although widespread, the mechanisms dictating protein partner identity and, therefore, the outcome of a switch have been determined for a limited number of systems. The Escherichia coli protein BirA undergoes a switch between posttranslational biotin attachment and transcription repression in response to cellular biotin demand. Moreover, the functional switch reflects formation of alternative mutually exclusive protein:protein interactions by BirA. Previous studies provided a set of alanine-substituted BirA variants with altered kinetic and equilibrium parameters of forming these interactions. In this work, DNase I footprinting measurements were employed to investigate the consequences of these altered properties for the outcome of the BirA functional switch. The results support a mechanism in which BirA availability for DNA binding and, therefore, transcription repression is controlled by the rate of the competing protein:protein interaction. However, occupancy of the transcriptional regulatory site on DNA by BirA is exquisitely tuned by the equilibrium constant governing its homodimerization.

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Section: Discussionsupporting

confidence: 61%

“…2) [13–16]. The BirA homodimer that functions in transcription regulation is formed by side-by-side antiparallel alignment of the central domain β-sheets of each monomer to form an extended intermolecular sheet.…”

Section: Introductionmentioning

confidence: 99%

Protein:Protein Interactions in Control of a Transcriptional Switch

Adikaram

Beckett

2013

Journal of Molecular Biology

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“…The deletion endpoints were based on structural modeling of B. subtilis BirA based on the crystal structure of S. aureus BirA (PDB 4DQ2) [7] (Fig. 6).…”

Section: Resultsmentioning

confidence: 99%

Successful Conversion of the Bacillus subtilis BirA Group II Biotin Protein Ligase into a Group I Ligase

Henke

Cronan

2014

PLoS ONE

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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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“…Higher expression of proteins required for de novo biotin synthesis, uptake and metabolic adaption may be processes that allow pathogens to survive during infection. Biotin is required for both folate uptake and metabolism (Pendini et al 2013) and folate starvation appears to be a key defense strategy of SCN resistant soybeans .…”

Section: Discussionmentioning

confidence: 99%

Annotation of Cultivar Variations at the Multigeneic Rhg1/Rfs2 Locus:

Hemmati

Geisler²,

Meksem³

et al. 2017

AJB

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Soybean (Glycine max (L.) Merr.) suffers yield loss due to root infection from soil infestation by Heterodera glycine I. (soybean cyst nematode SCN) and Fusarium virguliforme (Aoki; sudden death syndrome (SDS)). The major locus for SCN and SDS resistance has previously been identified as Rhg1/Rfs2 (chr18; LG G) (site reference). The objective of this experiment was to compare the Sanger DNA sequence of a resistant cultivar ('Forrest') and two susceptible cultivars ('Williams 82' and 'Asgrow A3244'). Sequences were downloaded from GenBank for Williams 82, Phytzome for A3244 and a newly sequenced BAC-B73P06 (82,157 bp) encompassing the Rfs2/Rhg1 locus. Using the resistant cultivars, 800 single nucleotide polymorphisms (SNPs) and 57 indels were identified. In contrast, the susceptible cultivars had just 12 SNPs and no indels between them. Polymorphisms were clustered within 59 kbp, divided into three sections. There were 5 predicted recombination breakpoints. The third and fourth breakpoints were located before gene 3 and after gene 5 (Glyma18g02680; the RLK at Rhg1/Rfs2) which were therefore inferred to be derived from Peking, within the Rhg1/Rfs2 region. Comparisons of SNPs identified in Illumina sequences from 31 semi-domesticated genomes showed 80% of the total SNPs in Forrest were found among the genomes. Annotation and gene prediction showed the BAC gene prediction encoded 9-10 genes. There were 31 SNPs within exons and 137 among introns. Just 11 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.SNPs caused amino acid changes. There were 5 SNPs in cis regulatory elements (CREs) and 14 in promoters. Polymorphisms indicated the regions that were introgressed from Peking had defined limits. Proteins across the region were highly conserved compared to non-coding regions, suggesting purifying selection occurred.

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Structural characterization of Staphylococcus aureus biotin protein ligase and interaction partners: An antibiotic target

Cited by 35 publications

References 55 publications

Protein:Protein Interactions in Control of a Transcriptional Switch

Protein:Protein Interactions in Control of a Transcriptional Switch

Successful Conversion of the Bacillus subtilis BirA Group II Biotin Protein Ligase into a Group I Ligase

Annotation of Cultivar Variations at the Multigeneic Rhg1/Rfs2 Locus:

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