A conserved regulatory mechanism in bifunctional biotin protein ligases

Wang, Jingheng; Beckett, Dorothy

doi:10.1002/pro.3182

Cited by 8 publications

(12 citation statements)

References 34 publications

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“…This finding agrees with our previous work which has demonstrated the apo-protein to be monomeric by small angle X-ray scattering assay 29 and crystallises as a single subunit 24 . It also agrees with recent work conducted on Sa BirA from the Newman strain reported by Wang and Beckett 25 where analytical ultracentrifugation (AUC) failed to detect homodimerization. This is in contrast to our previous AUC datum where dimerisation of apo- Sa BirA from Mu50 was observed 29 .…”

Section: Discussionsupporting

confidence: 92%

“…Several groups have now reported studies characterising BirA from S. aureus 24,25,27,29,34 . However, these studies have used genes encoding birA that have been cloned from different strains bearing different sequences making it difficult to directly compare the findings between studies.…”

Section: Resultsmentioning

confidence: 99%

“…A multiple sequence alignment was performed upon 26 non-redundant Sa BirA sequences (Supporting Fig. S7), including Mu50 (used in this study and in 24,29,34 ), Newman (used in the experiments reported in 25,27 ) and the well-studied NCTC 8325 strain. The alignment indicated that the sequence of Mu50 BirA is highly represented amongst the S. aureus genomes analysed.…”

Section: Resultsmentioning

confidence: 99%

“…S1B). Both proteins undergo analogous conformational changes that define the ordered ligand binding mechanism 23–25 . Like Ec BirA, Sa BirA is a biotin-dependent transcriptional repressor of biotin biosynthesis 26,27 .…”

Section: Introductionmentioning

confidence: 99%

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Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus

Satiaputra

Sternicki

Hayes

et al. 2019

Sci Rep

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An adequate supply of biotin is vital for the survival and pathogenesis of Staphylococcus aureus . The key protein responsible for maintaining biotin homeostasis in bacteria is the biotin retention protein A (BirA, also known as biotin protein ligase). BirA is a bi-functional protein that serves both as a ligase to catalyse the biotinylation of important metabolic enzymes, as well as a transcriptional repressor that regulates biotin biosynthesis, biotin transport and fatty acid elongation. The mechanism of BirA regulated transcription has been extensively characterized in Escherichia coli , but less so in other bacteria. Biotin-induced homodimerization of E. coli BirA ( Ec BirA) is a necessary prerequisite for stable DNA binding and transcriptional repression. Here, we employ a combination of native mass spectrometry, in vivo gene expression assays, site-directed mutagenesis and electrophoretic mobility shift assays to elucidate the DNA binding pathway for S. aureus BirA ( Sa BirA). We identify a mechanism that differs from that of Ec BirA, wherein Sa BirA is competent to bind DNA as a monomer both in the presence and absence of biotin and/or MgATP, allowing homodimerization on the DNA. Bioinformatic analysis demonstrated the Sa BirA sequence used here is highly conserved amongst other S. aureus strains, implying this DNA-binding mechanism is widely employed.

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Section: Discussionsupporting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus

Satiaputra

Sternicki

Hayes

et al. 2019

Sci Rep

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“…C), and exclusively depends on binding its co‐repressor, bio‐5'‐AMP to self‐dimerize (Fig. D) (Wang and Beckett, ), the SaBirA requires the presence of N‐terminal wHTH motif for its full BPL activity (Henke and Cronan, ). It is somewhat different from that of the EcBirA, a paradigm type II BPL, whose enzymatic function is independent of its DNA‐binding activity.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure and acetylation of BioQ suggests a novel regulatory switch for biotin biosynthesis in Mycobacterium smegmatis

Wei

Zhang

Gao

et al. 2018

Molecular Microbiology

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Biotin (vitamin B7), a sulfur-containing fatty acid derivative, is a nutritional virulence factor in certain mycobacterial species. Tight regulation of biotin biosynthesis is important because production of biotin is an energetically expensive process requiring 15-20 equivalents of ATP. The Escherichia coli bifunctional BirA is a prototypical biotin regulatory system. In contrast, mycobacterial BirA is an unusual biotin protein ligase without DNA-binding domain. Recently, we established a novel two-protein paradigm of BioQ-BirA. However, structural and molecular mechanism for BioQ is poorly understood. Here, we report crystal structure of the M. smegmatis BioQ at 1.9 Å resolution. Structure-guided functional mapping defined a seven residues-requiring motif for DNA-binding activity. Western blot and MALDI-TOF MS allowed us to unexpectedly discover that the K47 acetylation activates crosstalking of BioQ to its cognate DNA. More intriguingly, excess of biotin augments the acetylation status of BioQ in M. smegmatis. It seems likely that BioQ acetylation proceeds via a non-enzymatic mechanism. Mutation of this acetylation site K47 in BioQ significantly impairs its regulatory role in vivo. This explains in part (if not all) why BioQ has no detectable requirement of the presumable bio-5'-AMP effecter, which is a well-known ligand for the paradigm E. coli BirA regulator system. Unlike the scenario seen with E. coli carrying a single biotinylated protein, AccB, genome-wide search and Streptavidin blot revealed that no less than seven proteins require the rare post-translational modification, biotinylation in M. smegmatis, validating its physiological demand for biotin at relatively high level. Taken together, our finding defines a novel biotin regulatory machinery by BioQ, posing a possibility that development of new antibiotics targets biotin, the limited nutritional virulence factor in certain pathogenic mycobacterial species.

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Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation

Cronan

2023

Proteins

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Biotin (vitamin H or B7) is a coenzyme essential for all forms of life. Biotin has biological activity only when covalently attached to a few key metabolic enzyme proteins. Most organisms have only one attachment enzyme, biotin protein ligase (BPL), which attaches biotin to all target proteins. The sequences of these proteins and their substrate proteins are strongly conserved throughout biology. Structures of both the biotin ligase‐ and biotin‐acceptor domains of mammals, plants, several bacterial species, and archaea have been determined. These, together with mutational analyses of ligases and their protein substrates, illustrate the exceptional specificity of this protein modification. For example, the Escherichia coli BPL biotinylates only one of the >4000 cellular proteins. Several bifunctional bacterial biotin ligases transcriptionally regulate biotin synthesis and/or transport in concert with biotinylation. The human BPL has been demonstrated to play an important role in that mutations in the BPL encoding gene cause one form of the disease, biotin‐responsive multiple carboxylase deficiency. Promiscuous mutant versions of several BPL enzymes release biotinoyl‐AMP, the active intermediate of the ligase reaction, to solvent. The released biotinoyl‐AMP acts as a chemical biotinylation reagent that modifies lysine residues of neighboring proteins in vivo. This proximity‐dependent biotinylation (called BioID) approach has been heavily utilized in cell biology.

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A conserved regulatory mechanism in bifunctional biotin protein ligases

Cited by 8 publications

References 34 publications

Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus

Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus

Crystal structure and acetylation of BioQ suggests a novel regulatory switch for biotin biosynthesis in Mycobacterium smegmatis

Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation

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