Firmicutes-enriched IS1447 represents a group of IS3-family insertion sequences exhibiting unique + 1 transcriptional slippage

Abstract

BackgroundBacterial insertion sequences (ISs) are ubiquitous mobile genetic elements that play important roles in genome plasticity, cell adaptability, and function evolution. ISs of various families and subgroups contain significantly diverse molecular features and functional mechanisms that are not fully understood.ResultsIS1447 is a member of the widespread IS3 family and was previously detected to have transposing activity in a typical thermophilic and cellulolytic microorganism Clostridium thermocellum. Phylogenetic analysis showed that IS1447-like elements are widely distributed in Firmicutes and possess unique features in the IS3 family. Therefore, IS1447 may represent a novel subgroup of the IS3 family. Unlike other well-known IS3 subgroups performing programmed − 1 translational frameshifting for the expression of the transposase, IS1447 exhibits transcriptional slippage in both the + 1 and − 1 directions, each with a frequency of ~ 16%, and only + 1 slippage results in full-length and functional transposase. The slippage-prone region of IS1447 contains a run of nine A nucleotides following a stem-loop structure in mRNA, but mutagenesis analysis indicated that seven of them are sufficient for the observed slippage. Western blot analysis indicated that IS1447 produces three types of transposases with alternative initiations. Furthermore, the IS1447-subgroup elements are abundant in the genomes of several cellulolytic bacteria.ConclusionOur result indicated that IS1447 represents a new Firmicutes-enriched subgroup of the IS3 family. The characterization of the novel IS3-family member will enrich our understanding of the transposition behavior of IS elements and may provide insight into developing IS-based mutagenesis tools for thermophiles.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1304-8) contains supplementary material, which is available to authorized users.

Tailoring Genetic Elements of the Plasmid-Driven T7 System for Stable and Robust One-Step Cloning and Protein Expression in Broad Escherichia coli

“…coli native polymerase would perform transcriptional slippage, which implies that the polymerase transcribed longer or shorter RNA sequences than the target template, either during the initiation or elongation process, especially for which containing the homopolymeric sequences ( i.e. , T or A) . The PDT7m with insertion of TTTT conferred a T-rich homopolymer region to the transcriptional slippage, occurring to escape the early translational stop.…”

“…A previous report has proven that E. coli native polymerase would perform transcriptional slippage, which implies that the polymerase transcribed longer or shorter RNA sequences than the target template, either during the initiation or elongation process, especially for which containing the homopolymeric sequences (i.e., T or A). 14 The PDT7m with insertion of TTTT conferred a T-rich homopolymer region to the transcriptional slippage, occurring to escape the early translational stop. Moreover, no other mutations existed in the plasmid; thus, a trace amount of T7RNAP was sufficient to support the T7 orthogonality, leading to an increase in the fluorescence intensity.…”

Targeting the chromatin structural changes of antitumor immunity

“…The Tn5 transposon is the transposon of the IS4 family [ 196 ]. The IS4 family is divided into several subgroups, in which the subgroup of IS50 contains 19 transposon elements [ 197 ]. Tn5 transposase recognizes the mosaic end (ME) sequence of 19 bp on both sides of the DNA segment.…”