Targeted and proximity-dependent promiscuous protein biotinylation by a mutant Escherichia coli biotin protein ligase

doi:10.1016/j.jnutbio.2005.03.017

The Journal of Nutritional Biochemistry

Volume 16, Issue 7, July 2005, Pages 416-418

https://doi.org/10.1016/j.jnutbio.2005.03.017 Get rights and content

Abstract

A method for general protein biotinylation by enzymatic means has been developed. A mutant form (R118G) of the biotin protein ligase (BirA) of Escherichia coli is used and biotinylation is thought to proceed by chemical acylation of protein lysine side chains by biotinoyl-5′-AMP released from the mutant protein. Bovine serum albumin, chloramphenicol acetyltransferase, immunoglobulin chains and RNAse A as well as a large number of E. coli proteins have been biotinylated. The biotinylation reaction is proximity dependent in that the extent of biotinylation is much greater when the ligase is coupled to the acceptor protein than when the acceptor is free in solution. This is presumably due to rapid hydrolysis of the acylation agent, biotinoyl-5′-AMP. Therefore, when the mutant ligase is attached to one partner involved in a protein–protein interaction, it can be used to specifically tag the other partner with biotin, thereby permitting facile detection and recovery of the proteins by existing avidin/streptavidin technology.

References (4)

A. Chapman-Smith et al.
The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity
Trends Biochem Sci
(1999)
E. Choi-Rhee et al.
Promiscuous protein biotinylation by Escherichia coli biotin protein ligase
Protein Sci
(2004)

There are more references available in the full text version of this article.

Cited by (59)

An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry-Based Secretomics
2023, Molecular and Cellular Proteomics
The active release of proteins into the extracellular space and the proteolytic cleavage of cell surface proteins are key processes that coordinate and fine-tune a multitude of physiological functions. The entirety of proteins that fulfill these extracellular tasks are referred to as the secretome and are of special interest for the investigation of biomarkers of disease states and physiological processes related to cell-cell communication. LC-MS–based proteomics approaches are a valuable tool for the comprehensive and unbiased characterization of this important subproteome. This review discusses procedures, opportunities, and limitations of mass spectrometry–based secretomics to better understand and navigate the complex analytical landscape for studying protein secretion in biomedical science.
Anti-SARS-CoV-1 and −2 nanobody engineering towards avidity-inspired therapeutics
2022, Nano Today
Citation Excerpt :
In the genetic synthesis approach, aminoacyl tRNA synthetases (aaRS) are used to recognize and replace specific codons (e.g., amber UAG) with an unnatural amino acid that bears the required orthogonal reactive handle [153]. Enzymatic approaches such as proximity-dependent biotinylation [154–157] and sortase A (Srt A) transpeptidation [158–161] facilely append handles necessary for multimerizing nanobodies on nanocarriers. For instance, in proximity-dependent biotinylation (Fig. 6B), enzymes such as biotin ligase (BirA) attach biotin molecules via nucleophilic interaction onto Avi-tag (GLNDIFEAQKIEWHE) bearing proteins using Mg2+ and ATP as cofactors [162].
In the past two decades, the emergence of coronavirus diseases has been dire distress on both continental and global fronts and has resulted in the search for potent treatment strategies. One crucial challenge in this search is the recurrent mutations in the causative virus spike protein, which lead to viral escape issues. Among the current promising therapeutic discoveries is the use of nanobodies and nanobody-like molecules. While these nanobodies have demonstrated high-affinity interaction with the virus, the unpredictable spike mutations have warranted the need for avidity-inspired therapeutics of potent inhibitors such as nanobodies. This article discusses novel approaches for the design of anti-SARS-CoV-1 and −2 nanobodies to facilitate advanced innovations in treatment technologies. It further discusses molecular interactions and suggests multivalent protein nanotechnology and chemistry approaches to translate mere molecular affinity into avidity.
Protein interaction networks of the mammalian core clock proteins
2022, Advances in Protein Chemistry and Structural Biology
Citation Excerpt :
One such method, which is the BioID method, is developed to overcome technical problems to detect weak or transient interactions using conventional screening methods. This method is based on proximity-dependent cellular biotinylation by a promiscuous bacterial biotin ligase (E. coli BirA R118G, shortly called BioID) (Choi-Rhee, Schulman, & Cronan, 2004; Cronan, 2005) which is fused to a bait protein to biotinylate the proteins in close proximity in living cells (Roux, Kim, Raida, & Burke, 2012). Therefore, in contrast to conventional approaches, BioID method is one of the most suitable way to label interactions in the most native environment.
Circadian rhythm is a 24-h cycle that regulates the biochemical and behavioral changes of organisms. It controls a wide range of functions, from gene expression to behavior, allowing organisms to anticipate daily changes in their environment. In mammals, circadian rhythm is generated by a complex transcriptional and translational feedback loop mechanism. The binding of CLOCK/BMAL1 heterodimer to the E-box of DNA located within the promoter region initiates transcription of clock control genes including the transcription of the other two core clock genes of Periods (Pers) and Cryptochromes (Crys). Then PERs and CRYs along with casein kinase 1ɛ/Δ translocate into the nucleus where they suppress CLOCK/BMAL1 transactivation and, in turn, clock-regulated gene expression. Various clock components must be operational to aid in their stabilization and period extension in circadian rhythm. In this review, we have highlighted the recent progress for the core clock interacting proteins to maintain and to stabilize circadian rhythm in mammals.
Proximity dependent biotinylation: Key enzymes and adaptation to proteomics approaches
2020, Molecular and Cellular Proteomics
The study of protein subcellular distribution, their assembly into complexes and the set of proteins with which they interact with is essential to our understanding of fundamental biological processes. Complementary to traditional assays, proximity-dependent biotinylation (PDB) approaches coupled with mass spectrometry (such as BioID or APEX) have emerged as powerful techniques to study proximal protein interactions and the subcellular proteome in the context of living cells and organisms. Since their introduction in 2012, PDB approaches have been used in an increasing number of studies and the enzymes themselves have been subjected to intensive optimization. How these enzymes have been optimized and considerations for their use in proteomics experiments are important questions. Here, we review the structural diversity and mechanisms of the two main classes of PDB enzymes: the biotin protein ligases (BioID) and the peroxidases (APEX). We describe the engineering of these enzymes for PDB and review emerging applications, including the development of PDB for coincidence detection (split-PDB). Lastly, we briefly review enzyme selection and experimental design guidelines and reflect on the labeling chemistries and their implication for data interpretation.
Extracellular Proximity Labeling Reveals an Expanded Interactome for the Matrisome Protein TIMP2
2024, Research Square
Interactions of drosophila cryptochrome
2024, Photochemistry and Photobiology

View all citing articles on Scopus

^☆: This paper was presented at the international symposium “Vitamins as Regulators of Genetic Expression: Biotin as a Model” NAFTA Satellite Meeting to the XXV National Congress of Biochemistry held on December 3–4, 2004, in Ixtapa, Zihuatanejo, Mexico. This meeting was sponsored by Sociedad Mexicana de Bioquimica A.C.; Programa de Doctorado en Ciencias Biomedicas, Universidad Nacional Autonoma de Mexico; Laboratorios Roche–Syntex, Mexico; and Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico.

View full text

Article preview

The Journal of Nutritional Biochemistry

Abstract

References (4)

The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity

Trends Biochem Sci

Promiscuous protein biotinylation by Escherichia coli biotin protein ligase

Protein Sci

Cited by (59)

An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry-Based Secretomics

Anti-SARS-CoV-1 and −2 nanobody engineering towards avidity-inspired therapeutics

Protein interaction networks of the mammalian core clock proteins

Proximity dependent biotinylation: Key enzymes and adaptation to proteomics approaches

Extracellular Proximity Labeling Reveals an Expanded Interactome for the Matrisome Protein TIMP2

Interactions of drosophila cryptochrome

Research articleTargeted and proximity-dependent promiscuous protein biotinylation by a mutant Escherichia coli biotin protein ligase☆

Abstract

Trends Biochem Sci

Promiscuous protein biotinylation by Escherichia coli biotin protein ligase

Protein Sci

Research article
Targeted and proximity-dependent promiscuous protein biotinylation by a mutant Escherichia coli biotin protein ligase☆