Transposable elements Class

These substances resemble 3-lactam molecules (Figure 43-7) but they have very weak antibacterial action. They are potent inhibitors of many but not all bacterial 3 lactamases and can protect hydrolyzable penicillins from inactivation by these enzymes. -Lactamase inhibitors are most active against Ambler class A lactamases (plasmid-encoded transposable element [ ] lactamases in particular), such as those produced by staphylococci, H influenzae, N gonorrhoeae, salmonella, shigella, E coli, and pneumoniae. They are not good inhibitors of class lactamases, which typically are chromosomally encoded and inducible, produced by enterobacter, citrobacter, serratia, and pseudomonas, but they do inhibit chromosomal 3 lactamases of bacteroides and moraxella. 

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). 

All of the mammalian transposable elements that have been characterized to date seem to be the result of transpositions that proceeded through an RNA intermediate. This process is known as retrotransposition or retroposition. Three classes of these retrotransposable elements are known in mammals (1) SINEs, or short interspersed repeated sequences such as the human Alu family and rodent Bl (2) LINEs, or long interspersed repeated sequences such as LI in a variety of mammalian species and (3) retrovirus-like elements, such as THE 1 in humans and mys and IAP in rodents. Retrovirus-like elements have long terminal repeats (LTRs) that often surround two open reading frames (ORFs) like those of retroviruses, but they lack the ability to leave one cell and enter another. LINEs also have two ORFs, but have no LTRs. SINEs have no LTRs and no ORFs. Transposition of all of these elements must involve reverse transcription of the RNA intermediate in some cases the required reverse transcriptase is apparently encoded by the element itself. 

In general the definition of a transposable element is not that any one particular element has been proved to transpose, rather that a particular repetitive DNA sequence can be demonstrated to be interspersed in genomic DNA and have sequence similarity with established classes of trans-... 

The major forms of transposable elements in eukaryotes that lack terminal repeats belong to the class of retrotransposons. The LINEs and SINEs in mammals (long interspersed elements and short interspersed... 

In searching for new transposable elements, it is generally not possible to use DNA cross-hybridization to detect related elements from the same class, because the similarity is detectable only in the amino acid sequences. Instead, the features that are diagnostic of some transposable elements are the presence of terminal repeats, whether inverted or direct, and the amino acid sequence of the proteins they encode. Before a new transposable element can be classified, it is necessary to determine the DNA sequence of the element. 

Transposable elements have been demonstrated in many eukaryotes, including maize. Drosophila, yeast, and bacteria. Gene transposition in eukaryotic systems presents some strong similarities to and some distinct differences from transposition in bacteria. The first major distinction is that integration and excision are distinct processes in eukaryotes. Thus, the transposable element can be isolated in free form, often as a double-strand circular DNA. Second, replication of that DNA often involves the synthesis of an RNA intermediate. Both of these properties are seen in the retroviruses of vertebrates, perhaps the most widely studied class of eukaryotic transposable elements. 

Three different classes of transposable elements in bacteria, with general structures are shown in Figure 25.35. 

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). 

Transposable elements in eukaryotic cells show striking resemblances to retroviruses in sequence organization. The term retrotransposon is used to denote this class of elements. These similarities are illustrated in Figure 25.39 for two retroviruses Ty, a transposon of yeast copia and 412, transposable elements in Drosophila, and LAP, a transposon found in the mouse genome. 

Three classes of transposable elements are recognized in bacteria. 

Repeat elements are a significant port of almost any genome. Repetitive sequences can be primary divided into three classes local repeats (tandem repeats and simple sequence repeats), families of dispersed repeats (mostly Transposable Elements (TEs) and retrotransposed cellular genes), and segmental duplications (duplicated genomic fragments). 

Quesneville, H. Anxolabehere, D. (2001). Genetic algorithm-based model of evolutionary dynamics of class II transposable elements, J. Theor. Biol, Vol. 213, pp. 21-30. 

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