Firmicutes-enriched IS1447 represents a group of IS3-family insertion sequences exhibiting unique +\u20091 transcriptional slippage

Ya-Jun Liu,Chao Chen,Qiu Cui,Jie Zhang,Kuan Qi,Yingang Feng

doi:10.1186/s13068-018-1304-8

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.

Highlights

Bacterial insertion sequences (ISs) are ubiquitous mobile genetic elements that play important roles in genome plasticity, cell adaptability, and function evolution
Sequencing results suggested that the tdk gene was mutated by the insertion of IS1447, an endogenous Transposable elements (TEs) with a sequence length of 1447 bp, which was detected in C. thermocellum ATCC27405 during previous chemical mutagenesis [24]
Several thermophilic IS elements have been reported to have transposition activity, such as ISCbe4, ISCahy1 and IS1447 from Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor bescii, and Clostridium thermocellum, respectively [22,23,24], which provide insight into developing genetic tools for thermophiles based on endogenous genetic elements, such as the development of the Thermotargetron system for gene targeting based on a thermophilic group II intron [50]

Summary

Introduction

Bacterial insertion sequences (ISs) are ubiquitous mobile genetic elements that play important roles in genome plasticity, cell adaptability, and function evolution. Transposable elements (TEs) are ubiquitously present in nature [1] They can change their position in the genome and play critical roles in genome function and evolution [2, 3]. Some IS elements can implement the recoding of their Orfs via a programmed frameshifting strategy at the transcriptional or translational level [5, 9, 10]. In this way, a single DNA fragment can encode different functional Tpases. By controlling the expression intensity and interactions of the Tpases, the transposition activity and specificity of the IS may be regulated [11]

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Conclusion