Transposable Elements Dr. Nilansu Das Dept. of Microbiology Surendranath College

A transposable element is any genomic sequence Transposons A transposable element is any genomic sequence that possesses an intrinsic ability to mobilize

“Genome in flux” Concept Each Gene Has A Definite And Unvarying Location In A Particular Chromosome :A long-standing assumption about gene organization In the 1940s Barbara McClintock discovered regulatory elements that moved from one site to another and thereby affected gene expression in maize In contrast to other recombination events inside the cell movement of these elements occur at the same frequency in recA- and recA+ cells “Genome in flux”

What are Transposons ? Transposable genetic elements or transposons are segments of DNA that have the capacity to move from one location to another (i.e. jumping genes). Because they move around to different positions in the genome, they may cause mutations, increase or decrease in the amount of DNA at a particular position in the genome.

Phenotypic Manifestation of Transposition

Concept Many bacterial transposons contain easily recognizable genes, which may or may not exist elsewhere in the genome. Antibiotic resistance genes are common. Most antibiotic resistance transposons were originally designated by the abbreviation Tn followed by a number . (e.g. Tn10). The transposon first discovered did not contain any known host gene, and for historical reasons, they were called insertion sequences or IS elements, designated IS1, IS2 and so forth. Occassionally, transposons have been designated in nonstandard ways: δ, an element contained in the F plasmid Conventionally, mutation caused by transposition is designated as shown: lacZ87::Tn3 (Tn3 mediated transposition mutagenesis of lacZ gene)

Simplest transposable element carry a transposase gene flanked by recombination sites Transposon carry inverted repeats at the ends, varying in length from 25 to a few hundred bp. At the site of recombination, they create direct repeats. •The recombinase responsible for transposition are usually called transposases or integrases. •Sometimes they carry a few additional genes. Example, many bacterial DNA transposons carry antibiotic resistance gene.

Properties of Transposons Random movement : Transposable genetic elements can move from any DNA molecule to any other DNA molecule or even to another location on the same molecule. The movement is not totally random; there are preferred sites in a DNA molecule at which the transposable genetic element will insert. Not capable of self replication : The transposable genetic elements do not exist autonomously (exception - some transposable phages) and thus, to be replicated they must be a part of some other replicon.

Properties of Transposons Transposition mediated by site-specific recombination: Transposition requires little or no homology between the current location and the new site. The transposition event is mediated by a transposase coded by the transposable genetic element. Recombination that does not require homology between the recombining molecules is called site-specific or illegitimate or nonhomologous recombination.

Transposons can be autonomous or nonautonomous elements Autonomous transposons: carry a pair of terminal inverted repeats and a transposase gene; function independently Nonautonomous transposons: carry only the terminal inverted repeats; need the transposase encoded by autonomous transposons to enable transposition

Bacterial Transposable Elements (Mostly DNA transposable elements) Types of Transposable Elements Type II DNA Transposons, operate mostly through “cut and paste” mechanism Type I Retrotransposons, operate via RNA intermediate Bacterial Transposable Elements (Mostly DNA transposable elements) IS Elements Tn Elements Composite Noncomposite (IS elements as TIRs) (non-IS elements as TIRs)

Bacterial Transposable Elements Bacterial transposable elements were initially detected because of the genetic instability of phenotypes. The two classes of bacterial elements are insertion sequences or IS elements and Tn elements. Both of these classes are related to each other.  IS elements are a family of elements that range from 768 to 1426 bp in size and are represented in different copy number in bacterial chromosomes and on associated F factors.

Features of IS and Tn elements inverted repeats on each end of the element that range in size from 9-40 bp create duplications of the target site upon insertion; this duplication occurs at both ends of the elements and they are in a direct orientation composite transposons (Tns) can be created when two IS elements insert near each other; if the terminal repeats are used for further transposition then the internal sequences will be carried along Tns arise from IS elements; these may be identical or different IS elements; Tn5 is derived from IS50L andIS50R; these two elements differ by a single nucleotide change in IS50L which has eliminated its transposition ability the IS elements contain two genes that are essential for transposition, a transposase and a resolvase; the transposition functions in Tns are found in the IS region of the element Tns normally carry a drug resistance gene

Number of IS Elements in E. coli and F factors # in F factor IS1 8 - IS2 5 1 IS3 2 IS4

Biological relevance of transposons Transposons are present in the genomes of all life-forms Transposon-related sequences can make up huge fractions of the genome of an organism (50% of human and maize genome). Transposon content in different genomes is highly variable The genetic recombination mechanisms of transposition are also used for other functions, such as integration of some virus into the host genome and some DNA rearrangement to alter gene expression [V(D)J recombination].

Repetitive Elements Represent a Major Portion of Eukaryotic Genomes 100 75 % of genome >50 45 50 25 15 1 1.1 3.1 worms pombe cerevisiae fly human corn

Replicative Transposition 5’

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