Abstract: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 in… Show more
“…Repression complex assembly by the Ec BirA occurs in two steps including dimerization followed by bioO binding . Moreover, in the E. coli system, the large difference in the overall two‐step repression complex assembly energetics in the absence and presence of bio‐5′‐AMP results from the enhanced dimerization of holoBirA relative to apoBirA . Previous measurements suggest that this is not the case for Sa BirA.…”
Class II bifunctional biotin protein ligases (BirA), which catalyze post-translational biotinylation and repress transcription initiation, are broadly distributed in eubacteria and archaea. However, it is unclear if these proteins all share the same molecular mechanism of transcription regulation. In Escherichia coli the corepressor biotinoyl-5'-AMP (bio-5'-AMP), which is also the intermediate in biotin transfer, promotes operator binding and resulting transcription repression by enhancing BirA dimerization. Like E. coli BirA (EcBirA), Staphylococcus aureus, and Bacillus subtilis BirA (Sa and BsBirA) repress transcription in vivo in a biotin-dependent manner. In this work, sedimentation equilibrium measurements were performed to investigate the molecular basis of this biotin-responsive transcription regulation. The results reveal that, as observed for EcBirA, Sa, and BsBirA dimerization reactions are significantly enhanced by bio-5'-AMP binding. Thus, the molecular mechanism of the Biotin Regulatory System is conserved in the biotin repressors from these three organisms.
“…Repression complex assembly by the Ec BirA occurs in two steps including dimerization followed by bioO binding . Moreover, in the E. coli system, the large difference in the overall two‐step repression complex assembly energetics in the absence and presence of bio‐5′‐AMP results from the enhanced dimerization of holoBirA relative to apoBirA . Previous measurements suggest that this is not the case for Sa BirA.…”
Class II bifunctional biotin protein ligases (BirA), which catalyze post-translational biotinylation and repress transcription initiation, are broadly distributed in eubacteria and archaea. However, it is unclear if these proteins all share the same molecular mechanism of transcription regulation. In Escherichia coli the corepressor biotinoyl-5'-AMP (bio-5'-AMP), which is also the intermediate in biotin transfer, promotes operator binding and resulting transcription repression by enhancing BirA dimerization. Like E. coli BirA (EcBirA), Staphylococcus aureus, and Bacillus subtilis BirA (Sa and BsBirA) repress transcription in vivo in a biotin-dependent manner. In this work, sedimentation equilibrium measurements were performed to investigate the molecular basis of this biotin-responsive transcription regulation. The results reveal that, as observed for EcBirA, Sa, and BsBirA dimerization reactions are significantly enhanced by bio-5'-AMP binding. Thus, the molecular mechanism of the Biotin Regulatory System is conserved in the biotin repressors from these three organisms.
“…In fact, the more the extinction coefficient value of animal allergens is, the more the Tyr, Cys, and Trp amino acids (aromatic amino acids) in their sequence order. The computed extinction coefficient values are useful in the quantitative study of protein-protein and protein-ligand interactions in solution and are proportional to the binding strength [1, 41, 42].…”
Section: Discussionmentioning
confidence: 99%
“…Allergy can be emerged by several inflammatory symptoms such as rhinitis, urticaria, asthma, and anaphylactic immediate and late reactions [1, 2]. Mast cells and basophils have critical roles in allergy procedure and are subsequently activated by immune system components: antibodies of IgE class and T H 2-mediated pathways [3, 4].…”
<b><i>Background:</i></b> A large number of allergens are derived from plant and animal proteins. A major challenge for researchers is to study the possible allergenic properties of proteins. The aim of this study was in silico analysis and comparison of several physiochemical and structural features of plant- and animal-derived allergen proteins, as well as classifying these proteins based on Chou’s pseudo-amino acid composition (PseAAC) concept combined with bioinformatics algorithms. <b><i>Methods:</i></b> The physiochemical properties and secondary structure of plant and animal allergens were studied. The classification of the sequences was done using the PseAAC concept incorporated with the deep learning algorithm. Conserved motifs of plant and animal proteins were discovered using the MEME tool. B-cell and T-cell epitopes of the proteins were predicted in conserved motifs. Allergenicity and amino acid composition of epitopes were also analyzed via bioinformatics servers. <b><i>Results:</i></b> In comparison of physiochemical features of animal and plant allergens, extinction coefficient was different significantly. Secondary structure prediction showed more random coiled structure in plant allergen proteins compared with animal proteins. Classification of proteins based on PseAAC achieved 88.24% accuracy. The amino acid composition study of predicted B- and T-cell epitopes revealed more aliphatic index in plant-derived epitopes. <b><i>Conclusions:</i></b> The results indicated that bioinformatics-based studies could be useful in comparing plant and animal allergens.
“… 46 , 53 Recent DNase I footprint studies performed in the presence of BCCP provide support for this model. 55 Fig. 4 Competing protein:protein interactions.…”
Section: Switching Between Enzymatic and Repressor Functions Of Bplmentioning
Biotin is an essential micronutrient that acts as a co-factor for biotin-dependent metabolic enzymes. In bacteria, the supply of biotin can be achieved by de novo synthesis or import from exogenous sources. Certain bacteria are able to obtain biotin through both mechanisms while others can only fulfill their biotin requirement through de novo synthesis. Inability to fulfill their cellular demand for biotin can have detrimental consequences on cell viability and virulence. Therefore understanding the transcriptional mechanisms that regulate biotin biosynthesis and transport will extend our knowledge about bacterial survival and metabolic adaptation during pathogenesis when the supply of biotin is limited. The most extensively characterized protein that regulates biotin synthesis and uptake is BirA. In certain bacteria, such as Escherichia coli and Staphylococcus aureus, BirA is a bi-functional protein that serves as a transcriptional repressor to regulate biotin biosynthesis genes, as well as acting as a ligase to catalyze the biotinylation of biotin-dependent enzymes. Recent studies have identified two other proteins that also regulate biotin synthesis and transport, namely BioQ and BioR. This review summarizes the different transcriptional repressors and their mechanism of action. Moreover, the ability to regulate the expression of target genes through the activity of a vitamin, such as biotin, may have biotechnological applications in synthetic biology.
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