Ultrafast Protein Splicing is Common among Cyanobacterial Split Inteins: Implications for Protein Engineering

Department of Chemistry, Princeton University, 325 Frick Chemistry Laboratory, Princeton, New Jersey 08544, USA.
Journal of the American Chemical Society (Impact Factor: 11.44). 06/2012; 134(28):11338-41. DOI: 10.1021/ja303226x
Source: PubMed

ABSTRACT We describe the first systematic study of a family of inteins, the split DnaE inteins from cyanobacteria. By measuring in vivo splicing efficiencies and in vitro kinetics, we demonstrate that several inteins can catalyze protein trans-splicing in tens of seconds rather than hours, as is commonly observed for this autoprocessing protein family. Furthermore, we show that when artificially fused, these inteins can be used for rapid generation of protein α-thioesters for expressed protein ligation. This comprehensive survey of split inteins provides indispensable information for the development and improvement of intein-based tools for chemical biology.

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    • "The selected Ser+1 clones with b 10% spliced product had a flexible glycine residue at − 1 or − 2 in the N-extein and S(W/ Y)(P/C) in the C-extein. Both Tyr+2 and Trp+2 are preferred residues at this important position for splicing of the Npu DnaE intein when Cys+1 is present [11] [13] [19] [23] [24] [27] [32] [33]. The selection of amino acids known to affect protein structure (glycine in all Ser+1 selected clones and proline in 8 of 9 low-yield Ser+1 clones) suggests that slight changes in active-site geometry could contribute to the improved activity of the Npu DnaE intein with Ser+1. "
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    ABSTRACT: Inteins self-catalytically cleave out of precursor proteins while ligating the surrounding extein fragments with a native peptide bond. Much attention has been lavished on these molecular marvels with the hope of understanding and harnessing their chemistry for novel biochemical transformations including coupling peptides from synthetic or biological origins and controlling protein function. Despite an abundance of powerful applications, the use of inteins is still hampered by limitations in our understanding of their specificity (defined as flanking sequences that permit splicing) and the challenge of inserting inteins into target proteins. We examined the frequently used Nostoc punctiforme Npu DnaE intein after the C-extein cysteine nucleophile (Cys+1) was mutated to serine or threonine. Previous studies demonstrated reduced rates and/or splicing yields with the Npu DnaE intein after mutation of Cys+1 to Ser+1. In this study, genetic selection identified extein sequences with Ser+1 that enabled the Npu DnaE intein to splice with only a 5-fold reduction in rate compared to the wild-type Cys+1 intein and without mutation of the intein itself to activate Ser+1 as a nucleophile. Three different proteins spliced efficiently after insertion of the intein flanked by the selected sequences. We then used this selected specificity to achieve traceless splicing in a targeted enzyme at a location predicted by primary sequence similarity to only the selected C-extein sequence. This study highlights the latent catalytic potential of the Npu DnaE intein to splice with an alternative nucleophile and enables broader intein utility by increasing insertion site choices. (C) 2014 MRC Laboratory of Molecular Biology. Published by Elsevier Ltd.
    Journal of Molecular Biology 11/2014; 426(24). DOI:10.1016/j.jmb.2014.10.025 · 3.96 Impact Factor
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    ABSTRACT: Inteins catalyze a post-translational modification known as protein splicing, where the intein removes itself from a precursor protein and concomitantly ligates the flanking protein sequences with a peptide bond. Over the past two decades, inteins have risen from a peculiarity to a rich source of applications in biotechnology, biomedicine, and protein chemistry. In this review, we focus on developments of intein-related research spanning the last 5 years, including the three different splicing mechanisms and their molecular underpinnings, the directed evolution of inteins towards improved splicing in exogenous protein contexts, as well as novel applications of inteins for cell biology and protein engineering, which were made possible by a clearer understanding of the protein splicing mechanism.
    Cellular and Molecular Life Sciences CMLS 08/2012; 70(7). DOI:10.1007/s00018-012-1120-4 · 5.86 Impact Factor
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    ABSTRACT: Chemically modified proteins are invaluable tools for studying the molecular details of biological processes, and they also hold great potential as new therapeutic agents. Several methods have been developed for the site-specific modification of proteins, one of the most widely used being expressed protein ligation (EPL) in which a recombinant α-thioester is ligated to an N-terminal Cys-containing peptide. Despite the widespread use of EPL, the generation and isolation of the required recombinant protein α-thioesters remain challenging. We describe here a new method for the preparation and purification of recombinant protein α-thioesters using engineered versions of naturally split DnaE inteins. This family of autoprocessing enzymes is closely related to the inteins currently used for protein α-thioester generation, but they feature faster kinetics and are split into two inactive polypeptides that need to associate to become active. Taking advantage of the strong affinity between the two split intein fragments, we devised a streamlined procedure for the purification and generation of protein α-thioesters from cell lysates and applied this strategy for the semisynthesis of a variety of proteins including an acetylated histone and a site-specifically modified monoclonal antibody.
    Journal of the American Chemical Society 12/2012; 135(1). DOI:10.1021/ja309126m · 11.44 Impact Factor
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