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Ross K, Zerillo MM, Chandler M, Varani AM. Annotation and Comparative Genomics of Prokaryotic Transposable Elements. Methods Mol Biol 2024; 2802:189-213. [PMID: 38819561 DOI: 10.1007/978-1-0716-3838-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The data generated in nearly 30 years of bacterial genome sequencing has revealed the abundance of transposable elements (TE) and their importance in genome and transcript remodeling through the mediation of DNA insertions and deletions, structural rearrangements, and regulation of gene expression. Furthermore, what we have learned from studying transposition mechanisms and their regulation in bacterial TE is fundamental to our current understanding of TE in other organisms because much of what has been observed in bacteria is conserved in all domains of life. However, unlike eukaryotic TE, prokaryotic TE sequester and transmit important classes of genes that impact host fitness, such as resistance to antibiotics and heavy metals and virulence factors affecting animals and plants, among other acquired traits. This provides dynamism and plasticity to bacteria, which would otherwise be propagated clonally. The insertion sequences (IS), the simplest form of prokaryotic TE, are autonomous and compact mobile genetic elements. These can be organized into compound transposons, in which two similar IS can flank any DNA segment and render it transposable. Other more complex structures, called unit transposons, can be grouped into four major families (Tn3, Tn7, Tn402, Tn554) with specific genetic characteristics. This chapter will revisit the prominent structural features of these elements, focusing on a genomic annotation framework and comparative analysis. Relevant aspects of TE will also be presented, stressing their key position in genome impact and evolution, especially in the emergence of antimicrobial resistance and other adaptive traits.
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Affiliation(s)
- Karen Ross
- Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | | | - Mick Chandler
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Alessandro M Varani
- Department of Agricultural and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, Unesp - São Paulo State University, Jaboticabal, Brazil.
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Toxin-Antitoxin Gene Pairs Found in Tn 3 Family Transposons Appear To Be an Integral Part of the Transposition Module. mBio 2020; 11:mBio.00452-20. [PMID: 32234815 PMCID: PMC7157771 DOI: 10.1128/mbio.00452-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transposable elements (TEs) are important in genetic diversification due to their recombination properties and their ability to promote horizontal gene transfer. Over the last decades, much effort has been made to understand TE transposition mechanisms and their impact on prokaryotic genomes. For example, the Tn3 family is ubiquitous in bacteria, molding their host genomes by the paste-and-copy mechanism. In addition to the transposition module, Tn3 members often carry additional passenger genes (e.g., conferring antibiotic or heavy metal resistance and virulence), and three were previously known to carry a toxin-antitoxin (TA) system often associated with plasmid maintenance; however, the role of TA systems within the Tn3 family is unknown. The genetic context of TA systems in Tn3 members suggests that they may play a regulatory role in ensuring stable invasion of these Tns during transposition. Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tns). The Tn3 family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase and transposase. We report here that a number of Tn3 members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial persistence. At least six different TA gene pairs are associated with various Tn3 members. Our data suggest that several independent acquisition events have occurred. In contrast to most Tn3 family passenger genes, which are generally located away from the transposition module, the TA gene pairs abut the res site upstream of the resolvase genes. Although their role when part of Tn3 family transposons is unclear, this finding suggests a potential role for the embedded TA in stabilizing the associated transposon with the possibility that TA expression is coupled to expression of transposase and resolvase during the transposition process itself.
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Abstract
Transposons of the Tn3 family form a widespread and remarkably homogeneous group of bacterial transposable elements in terms of transposition functions and an extremely versatile system for mediating gene reassortment and genomic plasticity owing to their modular organization. They have made major contributions to antimicrobial drug resistance dissemination or to endowing environmental bacteria with novel catabolic capacities. Here, we discuss the dynamic aspects inherent to the diversity and mosaic structure of Tn3-family transposons and their derivatives. We also provide an overview of current knowledge of the replicative transposition mechanism of the family, emphasizing most recent work aimed at understanding this mechanism at the biochemical level. Previous and recent data are put in perspective with those obtained for other transposable elements to build up a tentative model linking the activities of the Tn3-family transposase protein with the cellular process of DNA replication, suggesting new lines for further investigation. Finally, we summarize our current view of the DNA site-specific recombination mechanisms responsible for converting replicative transposition intermediates into final products, comparing paradigm systems using a serine recombinase with more recently characterized systems that use a tyrosine recombinase.
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Peng D, Chen S, Ruan L, Li L, Yu Z, Sun M. Safety assessment of transgenic Bacillus thuringiensis with VIP insecticidal protein gene by feeding studies. Food Chem Toxicol 2007; 45:1179-85. [PMID: 17320261 DOI: 10.1016/j.fct.2006.12.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 10/12/2006] [Accepted: 12/22/2006] [Indexed: 11/18/2022]
Abstract
The aim of this study was to evaluate the toxicology safety of a genetically modified (GM) Bacillus thuringiensis with vegetative insecticidal protein (VIP) gene. Acute and subacute toxicity studies by using its powder preparation were conducted in Wistar rats. The result of the acute study showed the no-observable-adverse-effect level (NOAEL) of this GM B. thuringiensis powder preparation was greater than 5000 mg/kg body weight (BW). In the subacute study, the data analysis of body weight gain, food and water consumptions, clinical observations, haematology, serum biochemistry, organ weight ratios and histopathological findings did not show significant differences between control and treated groups. These results proved the NOAEL of this GM B. thuringiensis powder preparation in subacute test was greater than 5000 mg/kg BW. Since both the acute and subacute oral toxicity were not detected at the highest dose recommended by OECD guidelines, this GM B. thuringiensis could be generally regarded as safe for use in bio-pesticide industry.
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Affiliation(s)
- Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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Vanhooff V, Galloy C, Agaisse H, Lereclus D, Révet B, Hallet B. Self-control in DNA site-specific recombination mediated by the tyrosine recombinase TnpI. Mol Microbiol 2006; 60:617-29. [PMID: 16629665 DOI: 10.1111/j.1365-2958.2006.05127.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tn4430 is a distinctive transposon of the Tn3 family that encodes a tyrosine recombinase (TnpI) to resolve replicative transposition intermediates. The internal resolution site of Tn4430 (IRS, 116 bp) contains two inverted repeats (IR1 and IR2) at the crossover core site, and two additional TnpI binding motifs (DR1 and DR2) adjacent to the core. Deletion analysis demonstrated that DR1 and DR2 are not required for recombination in vivo and in vitro. Their function is to provide resolution selectivity to the reaction by stimulating recombination between directly oriented sites on a same DNA molecule. In the absence of DR1 and/or DR2, TnpI-mediated recombination of supercoiled DNA substrates gives a mixture of topologically variable products, while deletion between two wild-type IRSs exclusively produces two-noded catenanes. This demonstrates that TnpI binding to the accessory motifs DR1 and DR2 contributes to the formation of a specific synaptic complex in which catalytically inert recombinase subunits act as architectural elements to control recombination sites pairing and strand exchange. A model for the organization of TnpI/IRS recombination complex is presented.
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Affiliation(s)
- Virginie Vanhooff
- Unité de Génétique, Institut des Sciences de la Vie, Université Catholique de Louvain, 5/6 Place Croix du Sud, B-1348 Louvain-la-Neuve, Belgium
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McLeod SM, Waldor MK. Characterization of XerC- and XerD-dependent CTX phage integration in Vibrio cholerae. Mol Microbiol 2005; 54:935-47. [PMID: 15522078 DOI: 10.1111/j.1365-2958.2004.04309.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CTXphi is a filamentous bacteriophage that encodes cholera toxin and integrates site-specifically into the larger of the two Vibrio cholerae chromosomes. The CTXphi genome lacks an integrase; instead, its integration depends on the chromosome-encoded tyrosine recombinases XerC and XerD. During integration, recombination occurs between regions of homology in CTXphi and the V. cholerae chromosome. Here, we define the elements on the phage genome (attP) and bacterial chromosome (attB) required for CTXphi integration. attB is a short sequence composed of one binding site for XerC and XerD spanning the site of recombination. Together, XerC and XerD bind to two sites within attP. While one XerC/D binding site in attP spans the core recombination region, the other site is approximately 80 bp away. Although integration occurs at the core XerC/D binding site in attP, the second site is required for CTXphi integration, suggesting it performs an architectural role in the integration reaction. In vitro cleavage reactions showed that XerC and XerD are capable of cleaving attB and attP sequences; however, additional cellular processes such as DNA replication or Holliday junction resolution by a host resolvase may contribute to integration in vivo.
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Affiliation(s)
- Sarah M McLeod
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, Boston, MA 02111, USA
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Collis CM, Hall RM. Comparison of the structure–activity relationships of the integron-associated recombination sites attI3 and attI1 reveals common features. Microbiology (Reading) 2004; 150:1591-1601. [PMID: 15133120 DOI: 10.1099/mic.0.26596-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Incorporation of gene cassettes into integrons occurs by IntI-mediated site-specific recombination between a 59-base element (59-be) site in the cassette and an attI site in the integron. While the 59-be sites share common features and are recognized by several different IntI recombinases, the sequences of attI sites are not obviously related and are preferentially recognized by the cognate IntI. To determine the features of attI sites that are required for recombination proficiency, the structure–activity relationships of a second attI site, the attI3 site from the class 3 integron, were examined. The attI3 site was confined to within a region consisting of 68 bp from the integron backbone and 15 bp from the adjacent cassette. This region includes four IntI3-binding sites, as assessed by gel shift and methylation interference studies. Two of the binding sites are inversely oriented and constitute a simple site that includes the recombination crossover point. The two additional binding sites appear to be directly oriented and one of them is essential for efficient recombination of the attI3 site with a 59-be, but not for recombination with a second full-length attI3 site, which occurs at 100-fold lower frequency. The fourth site enhances attI3 with 59-be recombination 10-fold. The finding that the organization and overall properties of attI3 are very similar to those of attI1 indicates that these features are likely to be common to all attI sites.
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Affiliation(s)
- Christina M Collis
- CSIRO Molecular Science, Riverside Life Sciences Centre, Riverside Corporate Park, North Ryde, NSW 2113, Australia
| | - Ruth M Hall
- CSIRO Molecular Science, Riverside Life Sciences Centre, Riverside Corporate Park, North Ryde, NSW 2113, Australia
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Genka H, Nagata Y, Tsuda M. Site-specific recombination system encoded by toluene catabolic transposon Tn4651. J Bacteriol 2002; 184:4757-66. [PMID: 12169600 PMCID: PMC135285 DOI: 10.1128/jb.184.17.4757-4766.2002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2002] [Accepted: 06/05/2002] [Indexed: 11/20/2022] Open
Abstract
The 56-kb class II toluene catabolic transposon Tn4651 from Pseudomonas putida plasmid pWW0 is unique in that (i) its efficient resolution requires, in addition to the 0.2-kb resolution (res) site, the two gene products TnpS and TnpT and (ii) the 2.4-kb tnpT-res-tnpS region is 48 kb apart from the tnpA gene (M. Tsuda, K.-I. Minegishi, and T. Iino, J. Bacteriol. 171:1386-1393, 1989). Detailed analysis of the 2.4-kb region revealed that the tnpS and tnpT genes encoding the putative 323- and 332-amino-acid proteins, respectively, were transcribed divergently with an overlapping 59-bp sequence in the 203-bp res site. The motifs (the R-H-R-Y tetrad in domains I and II with proper spacing) commonly conserved in the integrase family of site-specific recombinases were found in TnpS. In contrast, TnpT did not show any significant amino acid sequence homology to the other proteins that are directly or indirectly involved in recombination. Analysis of site-specific recombination under the Escherichia coli recA cells indicated that (i) the site-specific resolution between the two copies of the res site on a single molecule was catalyzed by TnpS, (ii) the functional res site was located within a 95-bp segment, and (iii) TnpT appeared to have the role of enhancing the site-specific resolution. It was also found that TnpS catalyzed the site-specific recombination between the res sites located at two different molecules to form a cointegrate molecule. Site-specific mutagenesis of the conserved tyrosine residue in TnpS led to the loss of both the resolution and the integration activities, indicating that such a residue took part in both types of recombination.
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Affiliation(s)
- Hiroyuki Genka
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
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Baum JA, Gilmer AJ, Light Mettus AM. Multiple roles for TnpI recombinase in regulation of Tn5401 transposition in Bacillus thuringiensis. J Bacteriol 1999; 181:6271-7. [PMID: 10515914 PMCID: PMC103759 DOI: 10.1128/jb.181.20.6271-6277.1999] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tn5401 is a class II transposable element derived from the gram-positive bacterium Bacillus thuringiensis. The 4,837-bp transposon encodes a Tn3-like transposase (TnpA) and an integrase-like recombinase (TnpI) and is notable for its unusually long 53-bp terminal inverted repeats (TIRs). The tnpA and tnpI genes are transcribed from a common promoter, designated P(R), that is subject to negative regulation by TnpI. The TIRs of Tn5401 each contain a 38-bp sequence that can be aligned with the 38- to 40-bp TIR sequences of Tn3-like transposons and an adjacent 12-bp sequence that binds TnpI. This unique juxtaposition of TnpA and TnpI binding sites suggests that TnpI may regulate the binding or catalytic activity of TnpA. The results of the present study indicate that TnpI, in addition to functioning as a site-specific recombinase and as a transcriptional repressor, is required for TnpA binding to the TIRs of Tn5401.
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Affiliation(s)
- J A Baum
- Ecogen Inc., Langhorne, Pennsylvania 19047-3023, USA.
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Collis CM, Kim MJ, Stokes HW, Hall RM. Binding of the purified integron DNA integrase Intl1 to integron- and cassette-associated recombination sites. Mol Microbiol 1998; 29:477-90. [PMID: 9720866 DOI: 10.1046/j.1365-2958.1998.00936.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The site-specific recombinase Intl1, encoded by class 1 integrons, catalyses the integration and excision of gene cassettes by recognizing two classes of sites, the integron-associated attl1 site and the 59-base element (59-be) family of sites that are associated with gene cassettes. Intl1 includes the four conserved amino acids that are characteristic of members of the integrase family, and Intl1 proteins with single amino acid substitutions at each of these positions had substantially reduced catalytic activity, consistent with this classification. Intl1 was purified as a fusion protein and shown to bind to isolated attl1 or 59-be recombination sites. Binding to attl1 was considerably stronger than to a 59-be. Binding adjacent to the recombination cross-over point was not detected. A strong Intl1 binding site within attl1 was localized by both deletion and footprinting analysis to a 14 bp region 24-37 bp to the left of the recombination cross-over point, and this region is known to be critical for recombination in vivo (Recchia et al., 1994). An imperfect (13/15) direct repeat of this region, located 41-55 bp to the left of the recombination cross-over point, contains a weaker Intl1 binding site. Mutation of the stronger binding site showed that a single base pair change accounted for the difference in the strength of binding.
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Affiliation(s)
- C M Collis
- CSIRO Molecular Science, Sydney Laboratory, North Ryde, NSW, Australia
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Kholodii GY, Yurieva OV, Gorlenko ZM, Mindlin SZ, Bass IA, Lomovskay OL, Kopteva AV, Nikiforov VG. Tn5041: a chimeric mercury resistance transposon closely related to the toluene degradative transposon Tn4651. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 8):2549-2556. [PMID: 9274008 DOI: 10.1099/00221287-143-8-2549] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This paper reports the discovery and characterization of Tn5041, a novel-type transposon vehicle for dissemination of mercury resistance in natural bacterial populations. Tn5041 (14876 bp), identified in a Pseudomonas strain from a mercury mine, is a Tn3 family mercury resistance transposon far outside the Tn21 subgroup. As in other Tn3 family transposons, Tn5041 duplicates 5 bp of the target sequence following insertion. Tn5041 apparently acquired its mer operon as a single-ended relic of a transposon belonging to the classical mercury resistance transposons of the Tn21 subgroup. The putative transposase and the 47 bp terminal inverted repeats of Tn5041 are closely related to those of the toluene degradative transposon Tn4651 and fall into a distinct subgroup on the fringe of the Tn3 family. The amino acid sequence of the putative resolvase of Tn5041 resembles site-specific recombinases of the integrase family. Besides the mer operon and putative transposition genes, Tn5041 contains a 4 kb region that accommodates a number of apparently defective genes and mobile elements.
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Affiliation(s)
- G Ya Kholodii
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - O V Yurieva
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Zh M Gorlenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - S Z Mindlin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - I A Bass
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - O L Lomovskay
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - A V Kopteva
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - V G Nikiforov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
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Sanchis V, Agaisse H, Chaufaux J, Lereclus D. A recombinase-mediated system for elimination of antibiotic resistance gene markers from genetically engineered Bacillus thuringiensis strains. Appl Environ Microbiol 1997; 63:779-84. [PMID: 9023958 PMCID: PMC168370 DOI: 10.1128/aem.63.2.779-784.1997] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A TnpI-mediated site-specific recombination system to construct genetically modified Bacillus thuringiensis strains was developed. Recombinant B. thuringiensis strains from which antibiotic resistance genes can be selectively eliminated were obtained in vivo with a new vector based on the specific resolution site of transposon Tn4430. For example, a cryIC gene, whose product is active against Spodoptera littoralis, was introduced into B. thuringiensis Kto harboring a cryIA(c) gene active against Ostrinia nubilalis. The resulting strain had a broader activity spectrum than that of the parental strain. It contained only B. thuringiensis DNA and was free of antibiotic resistance genes. This should facilitate regulatory approval for its development as a commercial biopesticide.
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Affiliation(s)
- V Sanchis
- Unité de Biochimie Microbienne, Institut Pasteur, URA 1300 CNRS, Paris, France.
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Baum JA, Kakefuda M, Gawron-Burke C. Engineering Bacillus thuringiensis bioinsecticides with an indigenous site-specific recombination system. Appl Environ Microbiol 1996; 62:4367-73. [PMID: 8953709 PMCID: PMC168264 DOI: 10.1128/aem.62.12.4367-4373.1996] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The cry genes of Bacillus thuringiensis encode a diverse group of crystal-forming proteins that exhibit insecticidal activity, particularly against the larvae of lepidopteran, coleopteran, and dipteran insects. The efficacy of B. thuringiensis-based biopesticides may be improved through the genetic manipulation of these genes. A gene transfer system has been developed for the introduction and maintenance of cloned insecticidal cry genes on small plasmids in B. thuringiensis. This vector system combines a B. thuringiensis plasmid replicon and an indigenous site-specific recombination system that allows for the selective removal of ancillary or foreign DNA from the recombinant bacterium after introduction of the Cry-encoding plasmid. The site-specific recombination system is useful for engineering strains with unique combinations of cry genes, resulting in new active ingredients with improved insecticidal properties.
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Affiliation(s)
- J A Baum
- Ecogen, Inc., Langhorne, Pennsylvania 19047-3023, USA.
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