Expanding the Definition of Class 3 Inteins and Their Proposed Phage Origin

Abstract

This study determined which class the mycobacteriophage Catera Gp206 and Nocardioides sp. JS614 TOPRIM inteins belong to based on catalytic mechanism. The mycobacteriophage Catera Gp206 intein (starting with Ser 1 ) is a class 3 intein, and its Ser 1 residue is not required for splicing. Based on phylogenetic analysis, we propose that class 3 inteins arose from a single mutated intein that was spread by phage into predominantly helicase genes in various phages and their hosts.

Intermolecular domain swapping induces intein-mediated protein alternative splicing

“…This is further complicated by cross-reactions among nonorthogonal inteins. Additionally, inteins are flexible enzymes that can achieve protein splicing through diversified mechanisms 41 . Variations of protein-splicing mechanisms by intein and intein-related sequences are still increasing 41,42 .…”

“…Additionally, inteins are flexible enzymes that can achieve protein splicing through diversified mechanisms 41 . Variations of protein-splicing mechanisms by intein and intein-related sequences are still increasing 41,42 . As more extensive genomic, metagenomic and proteomic data are available at an increasingly rapid pace, we anticipate more inteins and intein-related sequences as well as diversified natural and contrived molecules produced by iPAS, which could advance our understanding of their biochemical and physiological roles and their biotechnological applications.…”

Recent progress in intein research: from mechanism to directed evolution and applications

“…These inteins therefore belong, from a mechanistic point of view, to class 1. A different intein (MP-Catera Gp206), on the other hand, which also has a nucleophilic side chain at position A:1 (Ser) together with the WCT triplet, belongs to class 3 because in this case, the F:4 Cys was essential for splicing [27]. These studies show that in some instances, the primary intein sequence alone cannot accurately predict its classification.…”

“…For example, the Tfus Tfu2914 and Nsp-JS614 TOPRIM inteins present a Cys residue at position A:1, indicative of class 1, as well as the WCT triplet, indicative of class 3. Mutagenetic studies revealed that the A:1 Cys was essential for the first step of the splicing reaction, whereas the F:4 Cys of the WCT triplet was not [26,27]. These inteins therefore belong, from a mechanistic point of view, to class 1.…”

Sequential formation of two branched intermediates during protein splicing of class three inteins

“…Class 3 inteins have an additional signature sequence (Table 1) consisting of a dispersed triplet: Trp B:12 , Cys F:4 , and Thr G:5 (Tori et al 2010). Previous studies indicated that mutation of Thr G:5 can have a minimal effect, while mutation of Trp B:12 more significantly impairs splicing, and mutation of Cys F:4 totally blocks splicing (Brace et al 2010; Tori et al 2010; Tori and Perler 2011). Another feature of class 3 inteins is Ser +1 or Thr +1 at the G:8 position instead of Cys +1 , which dominates this position in other intein classes (Brace et al 2010; Perler 2002; Southworth et al 2000; Tori et al 2010; Tori and Perler 2011).…”