High-throughput Purification of Affinity-tagged Recombinant Proteins

Abstract

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further biochemical analyses to obtain detailed insights into structure/function relationships. Advances in oligonucleotide-and gene synthesis technology make large-scale mutagenesis strategies increasingly feasible, including the substitution of target residues by all 19 other amino acids. Gain-or loss-of-function phenotypes then allow systematic conclusions to be drawn, such as the contribution of particular residues to catalytic activity, protein stability and/or protein-protein interaction specificity.In order to attribute the different phenotypes to the nature of the mutation -rather than to fluctuating experimental conditions -it is vital to purify and analyse the proteins in a controlled and reproducible manner. High-throughput strategies and the automation of manual protocols on robotic liquid-handling platforms have created opportunities to perform such complex molecular biological procedures with little human intervention and minimal error rates [1][2][3][4][5] .Here, we present a general method for the purification of His-tagged recombinant proteins in a high-throughput manner. In a recent study, we applied this method to a detailed structure-function investigation of TFIIB, a component of the basal transcription machinery. TFIIB is indispensable for promoter-directed transcription in vitro and is essential for the recruitment of RNA polymerase into a preinitiation complex [6][7][8] . TFIIB contains a flexible linker domain that penetrates the active site cleft of RNA polymerase [9][10][11] . This linker domain confers two biochemically quantifiable activities on TFIIB, namely (i) the stimulation of the catalytic activity during the 'abortive' stage of transcript initiation, and (ii) an additional contribution to the specific recruitment of RNA polymerase into the preinitiation complex 4,5,12 . We exploited the high-throughput purification method to generate single, double and triple substitution and deletions mutations within the TFIIB linker and to subsequently analyse them in functional assays for their stimulation effect on the catalytic activity of RNA polymerase 4 . Altogether, we generated, purified and analysed 381 mutants -a task which would have been time-consuming and laborious to perform manually. We produced and assayed the proteins in multiplicates which allowed us to appreciate any experimental variations and gave us a clear idea of the reproducibility of our results.This method serves as a generic protocol for the purification of His-tagged proteins and has been successfully used to purify other recombinant proteins. It is currently optimised for the purification of 24 proteins but can be adapted to purify up to 96 proteins. Video LinkThe video component of this article can be found at https://www.jove.com/video/4110/ Protocol PART A: High-throughput growth of bacterial cultures. Grow Bacteria Overnight in 2 ml of Autoinduction Medium...

The RNA Polymerase Factory and Archaeal Transcription

“…Over the past few years, several manufacturers have developed “cell lysis” reagents that break up cells by purely chemical means. These proprietary mixtures of various nonionic detergents are capable of perforating bacterial cell walls without denaturing soluble protein, which are thereby released into the supernatant and can thus either be screened directly or purified chromatographically (e.g., by affinity purification with paramagnetic beads ,, ). For purification of inclusion bodies (such as the archaeal RNAP large catalytic subunits), comprehensive bacterial cell lysis is additionally achieved through a combination of detergent lysis reagent and recombinant bacteriophage T4 lysozyme, an enzyme that displays a specific activity 250 times greater than that of chicken egg white lysozyme .…”