Insertion Sequence and Transposons

An IS is a discrete segment of DNA, commonly between 1 and 1.5 kb, that can transpose directly to new sites on the genome. An IS element usually has a short inverted repeat (IR) sequence at both ends (i.e., IRL and IRR). The sequences of IRL and IRR of each IS element are very similar, but not identical. The IR sequences, which can vary in length from 9 to 41 bp, are characteristic for the particular IS and are required for transposition. Transposition of an IS to a new site leads to a duplication of a small sequence of the target DNA. The size of the duplication is characteristic of the IS element, ranging from 2 to 13 bp. ISs encode only the protein(s) that is required for transposition. Most of the ISs encode a transposase (Tpase) that has a conserved triplet of amino acids, Asp (D), Asp, and Glu (E) (71). The Tpase, which binds and processes IR sequences during transposition, is encoded by a single or sometimes two orf that correspond to the entire length of the element. Some IS elements encode enzymes related to the serine and tyrosine site-specific recombinases or the rolling circle replicase (72). At least 19 different families of IS elements have been identified in prokary-otic genomes (71).

ISs are found on the chromosomes of many different sequenced bacterial and archaeal genomes (71). No IS element was identified in a few sequenced genomes, notably, Aeropyrumpernix K1, Aquifex aeolicus VF5, Bacillus subtillis 168, Buchnera sp. strain APS, Chlamydia muridarum, Chlamydia trachomatis D/UW-3/CX, C. trachomatis

MOPN, Chlamydophila pneumoniae AR39, C. pneumoniae CWL029, C. pneumoniae J138,Methanobacterium thermautotrophicum DH,Mycoplasmagenitalium G37,Mycoplasma pneumoniae M129, Pasteurella multocida PM70, Pyrococcus horikkoshii OT3, Pyrococcus abyssi, Rickettsiaprowazekii, Synechocystis sp. PCC6803, and Treponema pallidum subsp. pallidum. However, subsequent analysis by other workers have uncovered IS in R. prowazekii, P. abyssi, Synechocystis, A. pernix K1, C. muridarum, and C. trachomatis (71).

In some bacterial lineages, many IS elements are found in high copy numbers. The genomes of Bordetella pertussis and Bordetella parapertussis have 261 and 112 copies of different IS elements, respectively (73). These elements play an important role in chromosomal rearrangements and generation of pseudogenes in B. pertussis and B. para-pertussis (74). The genome of Burkholderia mallei with two chromosomes possesses 171 complete and partial IS elements accounting for about 3.1% of the genome. These elements likely have mediated extensive genome-wide insertions, deletions, and inversion mutations in B. mallei (75). Yersinia pestis is another genome with abundant IS elements. A total of 140 complete and partial IS elements amounting to 3.7% of the genome were identified (76). Of the 149 pseudogenes found in Y. pestis 51 are caused by IS-insertion mutations.

The complete genome sequence of two strains of Shigella flexneri serotype 2a, strain 2457T (77) and strain 301 (78) were determined and analyzed. Strain 2457T contains a total of 284 IS elements, which account for 6.7% (309.4 kb) of the chromosome. The 301 strain contains 247 complete and 67 partial IS elements. These elements are believed to be the major cause of the dynamic nature of the S. flexneri chromosome (77,78).

The genome of Leptospira borgpetersenii serovar Hardjobovis also has a diverse and high number of IS elements, amounting to more than 6% of its genome. This is significantly higher than that of Leptospira interrogans serovar Lai and serovar Copen-hageni, both around 2% of the genome (see Chapter 7). The IS elements in L. borgpetersenii play a major role in the generation of large number (161) of pseudogenes in the genome.

A transposon, unlike an IS element, is a more complex type of mobile genetic element. Transposons contain genes that encode proteins required for transposition and proteins that have other functions including, for example, resistance to antibiotics or heavy metals. An important group of transposons is the conjugative transposon (CTn), which is able to mobilize from one bacterial cell to another of the same, or different, species by a conjugation-like process that requires cell-to-cell contact (79). Conjuga-tive transposons are found in many bacterial genera, and are particularly common among the Gram-positive streptococci and enterococci. A number of well-characterized CTns are able to transfer to commensal bacteria of the human gastrointestinal tract in anaerobic filter matings (80). A major concern is that CTns with multiple antibiotic resistance genes transmitted to commensal bacteria could potentially then transfer the resistance genes to pathogens in the gastrointestinal tract.

Some of the conjugative transposons (e.g., Tn916 from Enterococcus faecalis and CTnDot from Bacteroides thetaiotaomicron) have been classified as integrative and conjugative elements (ICEs). ICEs are a heterogenous group of self-transmissible mobile genetic elements that can mobilize like a conjugative plasmid and integrate into a host chromosome like a lysogenic phage. Many ICEs contain antibiotic and metal resistance genes like transposons. They may also contain DNA repair genes and genes encoding virulence factors (81). ICEs promote genome plasticity and provide a major contribution to lateral gene flow in prokaryotes (81).

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