Features associated with horizontal transfer

Many examples exist in streptomycetes where horizontal transfer seems to have occurred (Egan et al. 1998; Wiener et al. 1998; Egan et al. 2001; Tolba et al. 2002) especially during evolution of sequences related to complex product biosynthesis. The mechanisms of such transfer are not fully elucidated, though several have been extensively investigated.

Mobile elements provide bacteria with the ability to acquire genetic material by horizontal transfer. At least some pathogenicity traits in scab disease are found to be mobilised through horizontal gene transfer (Bukhalid et al. 2002; Kers et al. 2005). Horizontal gene transfer can occur through a number of mechanisms in bacteria, typically enumerated as transformation – direct uptake of genetic material; conjugation – transfer between bacteria by direct cell to cell contact; and transduction - phage-borne gene transfer.

The classification of a particular element found in genomic material can be difficult since groups of researchers appear to use different terms and classifications

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depending on their focus. It has been recommended that mobile elements should be classified by the presence of the rather simple modular elements found in them (Toussaint and Merlin 2002). Those authors suggest the use of three module categories: features associated with transfer of genetic material between locations within a cell, features associated with transfer of genetic material outside the cell, and stability features.

Plasmids are natural vectors often found as independently-replicating covalently closed circular forms. In various organisms plasmids have been found to carry genes with clear selective advantages to the host such as symbiosis genes, antibiotic resistance or xenobiotic breakdown, and such selective advantage is thought to be essential in maintaining plasmids for example in Escherichia coli populations (Gordon 1992). Some plasmids can integrate into host chromosomes and these can be identified by the presence of characteristic plasmid reproduction genes. Transfer functions involve at minimum kil and kor genes, kor meaning ‘kill override’ (Kendall and Cohen 1987), because it encodes the repressor of the kil transfer gene. Without the repressor, the transfer gene overexpresses and causes cell death. The names given to these genes in the different mobile elements seem to vary wildly so it is easier to recognize them by conserved domains (Figure 1-3) than by similarities to named genes.

Figure 1-3 Bead-on-string view of conserved domain architecture of Pfam (Coggill et al. 2008) domains for plasmid kor and kil genes. Architecture of korSA (top), a kor gene from S. amobofaciens pSAM2 mobile element, and (bottom) traSA, kil gene from the same element.

The conserved domain called GntR after the first discovery of this kind of negative repressor (Bachi and Kornberg 1975) is described with Pfam model PF00392 which covers the N-terminal HTH region of GntR-like bacterial transcription factors. Kor appears to be a typical GntR-family regulator, as it has a ligand-binding domain at the C terminal of the primary sequence of the protein. UTRA is PF07702 and represents ‘UbiC transcription regulator-associated’ domain, and is a conserved ligand-binding domain. FtsK-SpoIIIE is the model PF01580, and it is found in a

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wide variety of proteins including FtsK cell division protein from Escherichia coli

and stage III sporulation protein E SpoIIIE in Bacillus subtilis, which is implicated in intracellular DNA transfer. Other distinctive sets of genes identify particular kinds of Streptomyces plasmid: pSAM2-type integrative elements have four ‘spread’ genes

spdABCD genes as well as xis excisionase and int integrase genes (Possoz et al.

2001).

Bacteriophages are bacteria-specific viruses and can transmit genes between strains of bacteria by mistakes in repackaging (transduction). Some can integrate into host chromosomes at characteristic sites and the integrated forms are known as prophages, and can be recognized by the presence of conserved domains such as phage baseplate assembly (PF04717), coat protein (PF05357), tail fibre protein (PF04630), terminase involved in DNA packaging (PF05876) and so on as well as the integrase genes for example rve (PF00665). After integration prophages may become defective by losing essential viral reproduction genes and may gradually lose the identifiable genes for phage function.

Site-specific integration of bacteriophage λ in Escherichia coli occurs at a site named

attB, between the gal and bio operons. This site is 30bp in length and contains a central region of 15bp where the recombination will take place (Gottesman and Weisberg 1971). Recombination is facilitated by both host and phage-encoded factors and the attB site is fused with a phage-encoded attP site to leave hybrid attL

and attR sites surrounding the prophage (Abremski and Gottesman 1982). In “Streptomyces coelicolor” A3(2), sites similar to attB have been found as part of the integration site of prophage C31 and integrating plasmids (Combes et al. 2002).

Insertion sequence (IS) elements are the smallest autonomously replicating elements, and usually consist of short sections of DNA flanked by direct repeats and encoding just one protein, the transposase that catalyzes their mobility. They duplicate within genomes and can gain mobility for horizontal transfer by integration into conjugative elements. Insertion sequences can catalyse mobilization of host chromosomes, for example IS21 in Escherichia coli (Willetts et al. 1981), and after internal duplication in a genome IS elements may facilitate larger rearrangements by providing regions of identical sequence at which homologous recombination can begin. Several kinds of IS are found as part of larger elements, such as conjugative transposons.

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Conjugative transposons have a recognisable structure with transposition elements flanking a cargo region, in which coding sequences can be transferred between strains. They were first discovered in Gram positive organisms Enterococcus faecalis and Streptococcus pneumoniae (Salyers et al. 1995). The majority of conjugative transposons so far studied use a tyrosine-recombinase and integrate in a non-site specific manner, with a preference for AT rich sequences (Osborn and Boltner 2002).

‘Genomic island’ seems to be used as a general term for regions with some indicators of mobility and includes toxin production islands such as in

Corynebacterium diphtheriae (Cerdeno-Tarraga et al. 2003) as well as the one identified in S. turgidiscabies Car8 (Kers et al. 2005). Integrated mobile elements such as plasmids and conjugative transposons may become a favourable target for integration of further elements (Dobrindt et al. 2004) to form genomic islands. A newly integrated mobile element may have sections of DNA with no selective advantage to the host organism. Whereas natural selection will eliminate genomes in which integration has interrupted essential gene functions, integration of further mobile elements within the bounds of the acquired material is less likely to be selected against. Acquisition of insertion sequences by integrated mobile elements may lead to new mobility traits for the element such as additional recombination enzymes which could allow the element to reach new gene targets (Toussaint and Merlin 2002).

In document Study of the complete genome sequence of Streptomyces scabies (or scabiei) 87 22 (Page 31-34)