Composite transposons

Several bacterial transposons, referred to as insertion elements (ISelements), consist only of a gene that codes for a transposition enzyme (i.e., transposase), flanked by short DNA segments called inverted repeats (Figure 18.16). (Inverted repeats are short palindromes.) More complicated bacterial transposable elements, called composite transposons, contain additional genes, several of which may code for antibiotic resistance. Because transposons can jump between bacterial chromosomes, plasmids, and viral genomes, transpositions are now believed to play an important role in the spread of antibiotic resistance among bacteria. 

Class I elements (Figure 25.35) encode a transposase but not a resolvase, and are of two types. The simplest is called an insertion sequence (IS), which consists simply of a gene for transposase, flanked by two short inverted repeat sequences of about 15 to 25 base pairs. A less simple structure, called a composite transposon, consists of a protein-encoding gene, such as a gene conferring antibiotic resistance, flanked by two insertion sequences, or IS-like elements. These elements may be in either identical or inverted orientations. 

Retroviruses of vertebrates are, perhaps, the most widely studied class of eukaryotic transposable elements. These RNA viruses use reverse transcriptase to synthesize a circular duplex DNA, which can integrate into many sites of the host cell chromosome. The integrated retroviral genome bears remarkable resemblance to a bacterial composite transposon (compare Figure 25.38 with Figure 25.35). 

Composite iransposons contain a central region flanked by two identical (or nearly identical) IS-like sequencea These IS-like sequences have either the same or an inverted orientation, and are themselves flanked by inverted repeats. It therefore appears that composite transposons arose from the combination of a stretch of gene-containing DNA (the central region) with two independent insertion sequencer... 

Nakatsu, C., Ng, J-, Singh, R., Straus, N. Wyndham, C. (1991)- Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences. Proceedings of the National Academy of Sciences USA, 88, 8312-16. 

Studies of overall genome composition based on reassociation kinetics (Simpson et ai, 1982 Cox et ai, 1990 Marx et a/., 2000) and analysis of fully sequenced bacterial artificial chromosome (BAC) clones from the 5. mansoni genome project show that platyhelminth genomes contain abundant highly and moderately repetitive sequence (Fig. 2.1). Much of the repetitive DNA comprises two classes of integrated mobile elements class I elements, which include long terminal repeat (LTR) retrotransposons and retroviruses, non-LTR retro-transposons and short interspersed nuclear elements (SINES) and transpose via an RNA intermediate, and class II elements (trans-posons), which transpose as DNA (Brindley et ai, 2003). Additionally, small dispersed or tandemly repeated sequences are common. A wide variety of these sequences have been isolated and characterized from a variety of taxa (Table 2.4). 

The structural analysis of polysaccharides involved in biofilm formation of S. epidermidis has been hampered repeatedly by difficulties with the specific identification and purification of the molecules involved in biofilm formation. Not infrequently, components from the media used to grow the bacteria have been purified and analyzed leading to erroneous conclusions [41, 87] for a review see also [88], A significant step forward in the purification and elucidation of composition and structure of the functionally important polysaccharides was the isolation of isogenic biofilm-negative transposon... 

It should be stressed that the drift pushing a region beyond the acceptable thresholds is not only influenced by mutational biases but also by recombination events and transposon insertions. While these factors may slow down, accelerate or alter the direction of the compositional drift, the final control is still exerted by natural selection. 

In the central section of the book. Parts 3 and 4 outline the compositional properties of the vertebrate genome, namely the compositional patterns of DNA molecules and of coding sequences, as well as the compositional correlations between coding and non-coding sequences, whereas Parts 5, 6 and 7 discuss the most important properties of the vertebrate genome the distributions of genes, of transposons and of integrated viral... 

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