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      Firmicutes-enriched IS 1447 represents a group of IS 3-family insertion sequences exhibiting unique + 1 transcriptional slippage

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          Abstract

          Background

          Bacterial 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.

          Results

          IS 1447 is a member of the widespread IS 3 family and was previously detected to have transposing activity in a typical thermophilic and cellulolytic microorganism Clostridium thermocellum. Phylogenetic analysis showed that IS 1447-like elements are widely distributed in Firmicutes and possess unique features in the IS 3 family. Therefore, IS 1447 may represent a novel subgroup of the IS 3 family. Unlike other well-known IS 3 subgroups performing programmed − 1 translational frameshifting for the expression of the transposase, IS 1447 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 IS 1447 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 IS 1447 produces three types of transposases with alternative initiations. Furthermore, the IS 1447-subgroup elements are abundant in the genomes of several cellulolytic bacteria.

          Conclusion

          Our result indicated that IS 1447 represents a new Firmicutes-enriched subgroup of the IS 3 family. The characterization of the novel IS 3-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 material

          The online version of this article (10.1186/s13068-018-1304-8) contains supplementary material, which is available to authorized users.

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          Most cited references52

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          ISfinder: the reference centre for bacterial insertion sequences

          ISfinder () is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. Another objective is to continuously monitor ISs to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. The site also contains extensive background information on ISs and transposons in general. Online tools are gradually being added. At present an online Blast facility against the entire bank is available. But additional features will include alignment capability, PsiBLAST and HMM profiles. ISfinder also includes a section on bacterial genomes and is involved in annotating the IS content of these genomes. Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication.
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            Recombineering: a powerful new tool for mouse functional genomics.

            Highly efficient phage-based Escherichia coli homologous recombination systems have recently been developed that enable genomic DNA in bacterial artificial chromosomes to be modified and subcloned, without the need for restriction enzymes or DNA ligases. This new form of chromosome engineering, termed recombinogenic engineering or recombineering, is efficient and greatly decreases the time it takes to create transgenic mouse models by traditional means. Recombineering also facilitates many kinds of genomic experiment that have otherwise been difficult to carry out, and should enhance functional genomic studies by providing better mouse models and a more refined genetic analysis of the mouse genome.
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              Insertion sequences.

              Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available.
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                Author and article information

                Contributors
                liuyj@qibebt.ac.cn
                qikuan@qibebt.ac.cn
                zhangjie7008@outlook.com
                chenchao@qibebt.ac.cn
                cuiqiu@qibebt.ac.cn
                fengyg@qibebt.ac.cn
                Journal
                Biotechnol Biofuels
                Biotechnol Biofuels
                Biotechnology for Biofuels
                BioMed Central (London )
                1754-6834
                1 November 2018
                1 November 2018
                2018
                : 11
                : 300
                Affiliations
                [1 ]ISNI 0000000119573309, GRID grid.9227.e, CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, , Chinese Academy of Sciences, ; Qingdao, China
                [2 ]GRID grid.410752.5, Dalian National Laboratory for Clean Energy, ; Dalian, China
                [3 ]ISNI 0000 0004 1797 8419, GRID grid.410726.6, University of Chinese Academy of Sciences, Chinese Academy of Sciences, ; Beijing, China
                [4 ]ISNI 0000 0001 2297 8753, GRID grid.252546.2, Present Address: Department of Biosystems Engineering, , Auburn University, ; Auburn, AL 36849 USA
                Author information
                http://orcid.org/0000-0002-0879-1316
                Article
                1304
                10.1186/s13068-018-1304-8
                6211511
                d6da48c2-c39e-4c1f-92a2-41cb5eec95e0
                © The Author(s) 2018

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 25 July 2018
                : 27 October 2018
                Funding
                Funded by: Strategic Priority Research Program of the Chinese Academy of Sciences
                Award ID: XDA 21060201
                Award Recipient :
                Funded by: National Key Technology Research and Development Program of China
                Award ID: 2015BAD15B05
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31570029
                Award ID: 31670735
                Award ID: 31661143023
                Award Recipient :
                Funded by: Key Technology Research and Development Program of Shandong
                Award ID: 2018GSF1160165
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100007129, Natural Science Foundation of Shandong Province;
                Award ID: ZR2016CB09
                Award Recipient :
                Funded by: the Major Program of Shandong Provincial Natural Science Foundation
                Award ID: ZR2018ZB0208
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2018

                Biotechnology
                transposable element (te),frameshift,lignocellulose,thermophilic,clostridium thermocellum

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