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Summary

This article illustrates the use of pulse-chase radio labeling in combination with site-specific photocrosslinking to monitor interactions between a protein of interest and other factors in E. coli. Unlike traditional chemical cross-linking methods, this approach generates high resolution “snapshots” of an ordered assembly pathway in a living cell.

Abstract

This article describes a method to detect and analyze dynamic interactions between a protein of interest and other factors in vivo. Our method is based on the amber suppression technology that was originally developed by Peter Schultz and colleagues¹. An amber mutation is first introduced at a specific codon of the gene encoding the protein of interest. The amber mutant is then expressed in E. coli together with genes encoding an amber suppressor tRNA and an amino acyl-tRNA synthetase derived from Methanococcus jannaschii. Using this system, the photo activatable amino acid analog p-benzoylphenylalanine (Bpa) is incorporated at the amber codon. Cells are then irradiated with ultraviolet light to covalently link the Bpa residue to proteins that are located within 3-8 Å. Photocrosslinking is performed in combination with pulse-chase labeling and immunoprecipitation of the protein of interest in order to monitor changes in protein-protein interactions that occur over a time scale of seconds to minutes. We optimized the procedure to study the assembly of a bacterial virulence factor that consists of two independent domains, a domain that is integrated into the outer membrane and a domain that is translocated into the extracellular space, but the method can be used to study many different assembly processes and biological pathways in both prokaryotic and eukaryotic cells. In principle interacting factors and even specific residues of interacting factors that bind to a protein of interest can be identified by mass spectrometry.

Introduction

It is often essential to identify and characterize interactions between a protein of interest and other cellular components to define its role in a biological pathway, to understand its assembly, or to elucidate its mechanism of action. A wide variety of approaches are commonly used to study protein-protein interactions, but all have their limitations. The simplest unbiased method to identify proteins that bind to a protein of interest is copurification (or coimmunoprecipitation) but this approach requires that a protein complex remain intact during the purification procedure. Weak or transient protein interactions can be stabilized through chemical cross-linking, but this method typically requires the use of compounds that link proteins through primary amines that are widely scattered in the protein sequence. Complicated cross-linking patterns that are difficult to interpret can be generated, especially when proteins of interest are components of multiprotein complexes. Furthermore, because the spacer arms of chemical cross-linkers generally exceed 10 Å in length, covalent bonds can be formed with proteins that are located in proximity to but do not interact directly with the protein of interest. Methods such as affinity chromatography and two-hybrid screens are also often useful to identify protein-protein interactions. The former approach, however, requires reproducing conditions that promote physiologically significant interactions and cannot be used to detect weak interactions. The latter approach requires that binding interactions can be replicated in the host organism and are maintained when a protein of interest and its binding partners are placed in the context of a fusion protein. Two-hybrid methods also tend to generate false-positive results². Once a protein-protein interaction has been established, considerable work is often required to map the site of interaction. Perhaps the most significant drawback of traditional approaches is that they do not provide any information about the temporal sequence of intermolecular interactions or the kinetics of binding.

This paper describes a simple method that overcomes some of the limitations of other approaches that are used to study protein-protein interactions. Initially a single amber mutation is introduced into the gene that encodes a protein of interest. The amber mutant is then coexpressed with an amber suppressor tRNA and an amino acyl-tRNA synthetase derived from Methanococcus jannaschii that have been engineered to incorporate the photoactivatable amino acid analog p-benzoylphenylalanine (Bpa) only at amber codons³. Irradiation of cells with long wavelength ultraviolet (UV) light (~365 nm) then facilitates formation of a covalent bond between Bpa and proteins that are within ~3-8 Å^4,5. In some experimental contexts, cross-links can also be formed between activated Bpa and nonprotein components of cells such as lipids and nucleic acids⁶. Molecules that are terminated at the amber codon should generally be easily distinguishable from the full-length protein on SDS-PAGE and cannot be cross-linked to other proteins. By subjecting cells to pulse-chase radiolabeling prior to cross-linking and then immunoprecipitating or affinity purifying cross-linking products, the sequence and duration of protein-protein interactions can be established. The ability to generate temporal information about intermolecular interactions is especially valuable to study the progression of a protein of interest through any ordered multistep assembly, trafficking or signaling pathway and to identify pathway intermediates. Like chemical cross-linking, site-specific cross-linking detects protein-protein interactions that occur under physiological conditions, but the introduction of a cross-linker at a single position facilitates the analysis of interactions between individual segments of a protein and other factors. This unique feature of site-specific cross-linking is especially advantageous when the protein of interest has multiple segments or domains that have the potential to interact with distinct binding partners. Furthermore, site-specific cross-linking can be used in combination with methods such as mass spectrometry to map the residues that mediate protein-protein interactions with precision. Although this method is optimized for use in E. coli, the incorporation of photactivatable amino acid analogs into proteins by amber suppression has been reported in Mycobacterium, yeast and mammalian cells^7-11. Thus, in principle our method can be used in other systems.

We have used this method extensively to identify intermolecular interactions that facilitate the biogenesis of EspP, an E. coli O157:H7 virulence factor. EspP is a member of a superfamily of proteins known as "autotransporters" that contain a large N-terminal extracellular domain ("passenger domain") and aC-terminal domain ("b domain") that folds into a cylindrical b barrel structure and anchors the protein to the outer membrane (OM)¹². The mechanism by which the passenger domain is translocated across the OM has been a long-standing mystery. Like all bacterial cell surface proteins, EspP must be transported across the inner membrane, shuttled across the periplasm (the space between the inner and outer membranes), and targeted to the OM in a series of ordered events. Following its translocation across the OM, the EspP passenger domain is also separated from the b domain by a proteolytic cleavage and released from the cell surface. By combining site-specific cross-linking with pulse-chase radiolabeling, we have shown that both domains of the protein initially interact with the molecular chaperone Skp in the periplasm⁶. Subsequently, discrete segments of the b domain interact in a stereospecific fashion with components of a heterooligomer called the Bam complex, which catalyzes the integration of b barrel proteins into the bacterial OM by an unknown mechanism. Perhaps most interestingly, we have found that the passenger domain is in contact with one of the Bam complex subunits (BamA) as it traverses the OM¹³. Our results have enabled us to construct a detailed model for autotransporter assembly¹⁴ and have implicated the Bam complex in the transport of the passenger domain across the OM.

Protocol

1. Plasmid Construction After cloning a gene that encodes a protein of interest into an appropriate expression vector, introduce amber mutations at desired locations using a site-directed mutagenesis kit. NOTE: Structural information and surface exposure predictions can serve as useful guides to determine the positions of mutations. Because the efficiency of amber suppression and cross-linking can vary considerably, amber mutations should be introduced at multiple positions. Furthermore, because Bpa is…

Representative Results

We used site-specific photocrosslinking to identify proteins that interact with EspP during its journey to the OM. In the experiments that are shown here, phenylalanine codons at residues 1113 and 1214 were replaced with amber codons. Both positions are located in the bdomain, which integrates into the OM and serves as a membrane anchor. The crystal structure of the EspPβ domain16 shows that the two residues are on the periplasmic side of the b barrel but are separated by ~120° (see …

Discussion

This paper describes a method that combines site-specific photocrosslinking with pulse-chase labeling to examine the dynamics of interactions between a protein of interest and other components of a living cell. The method is especially useful to study multistep processes in which the protein interacts sequentially with other factors. Unlike traditional chemical cross-linking approaches, site-specific photocrosslinking provides detailed information about the status of individual segments or even individual residues of a p…

Materials

QuikChange II Site-Directed Mutagenesis Kit	Agilent	200521
BPA (H-p-Bz-Phe-OH)	Bachem	F-2800
TRAN35S-LABEL, Metabolic Labeling Reagent (35S-L-methionine and 35S-L-cysteine, >1,000 Ci/mmol)	MP Biomedicals	51006
Spectroline SB-100P Super-High-Intensity UV Lamp, 365 nm	Spectronics Corporation	SB-110P
Spectroline Replacement Bulb 100S	Spectronics Corporation	11-992-15
Falcon Tissue Culture Plate, 6-well	Becton Dickinson Labware	353046
Disposable 125 ml Erlenmeyer flask	Corning	430421
Innova 3100 shaking water bath	New Brunswick Scientific	n.a.