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Chapter 33 : Genetics: Accessory Elements and Genetic Exchange

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Abstract:

It is clear that the acquisition, maintenance, and dissemination of accessory elements have been central to the ongoing success of staphylococci as pathogens. Staphylococci represent a salient illustration of the adaptability afforded to microorganisms by access to additional functions through gene transfer mechanisms. Although DNA can be introduced into staphylococci in the laboratory via each of the three traditional bacterial gene transfer mechanisms—transformation, transduction, and conjugation—the latter two are believed to be the most significant mediators of natural genetic exchange. Most staphylococcal plasmids can be categorized as one of three main classes based on physical/genetic organization and functional characteristics, although another group, the pSK639 family plasmids, should be considered a fourth class. Staphylococcal insertion sequences and transposons are discussed in this chapter. Gene transfer mechanisms, together with accessory elements such as plasmids, transposable elements, prophages, and pathogenicity and resistance islands, serve as catalysts for microbial evolution by providing access to a shared reservoir of niche-adaptive functions. However, just as importantly, the combination of comparative genomics and sequence-based strain typing is clarifying the relationships between clinical strains. These studies are providing a new perspective on the scope and importance of the accessory genome, demonstrating that variation in pathogenic potential largely does not reside in the core genome, but rather that it is primarily attributable to the complement of mobile accessory elements that are present.

Citation: Firth N, Skurray R. 2006. Genetics: Accessory Elements and Genetic Exchange, p 413-426. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch33

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Toxic Shock Syndrome Toxin 1
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Gene Expression and Regulation
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Mobile Genetic Elements
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Figures

Image of FIGURE 1
FIGURE 1

Maps of the RC plasmid family prototypes, pT181, pC194, pE194, and pSN2, and the mobilizable pT181 family plasmid, pC221 ( ); see text for additional references. Plasmid sizes are shown on the right. Genes (arrowed boxes) and loci encoding the following functions are indicated: , chloramphenicol resistance; , double-stranded origin of DNA replication; , erythromycin resistance; //, plasmid mobilization; , plasmid recombination/mobilization; ////, initiation of plasmid replication; , single-stranded origin of DNA replication; (K), tetracycline resistance. Restriction sites shown: A, I; C, I; E, RI; H, dIII; Hp, II; K, I; P, II; T, I; V, RV.

Citation: Firth N, Skurray R. 2006. Genetics: Accessory Elements and Genetic Exchange, p 413-426. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch33
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Image of FIGURE 2
FIGURE 2

Maps of representative pSK639 family plasmids, pSK639 and pSK818 ( ). The locations of IS copies are marked by solid boxes, and the position of the cointegrated pT181-like plasmid within pSK818 is indicated. Plasmid sizes are shown on the right. Genes (arrowed boxes) and loci encoding the following functions are indicated: , trimethoprim resistance; , plasmid mobilization; , plasmid recombination/mobilization; , initiation of plasmid replication; , single-stranded origin of DNA replication; (K), tetracycline resistance; , thymidylate synthetase. Restriction sites shown: B, II; E, RI; K, I; S, I; V, RV.

Citation: Firth N, Skurray R. 2006. Genetics: Accessory Elements and Genetic Exchange, p 413-426. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch33
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Image of FIGURE 3
FIGURE 3

Maps of representative β-lactamase/heavy metal multiresistance plasmids pI524, pSK23, pI258, and pI9789:: Tn ( ); see text for additional references. The family to which each plasmid belongs is shown in parentheses on the left, and plasmid sizes are indicated on the right. The positions of transposons are shown above each map. Open and solid boxes denote copies of IS and IS, respectively. Selected loci encoding the following functions are indicated beneath the maps: , aminoglycoside resistance; , arsenic resistance; , penicillin resistance; , cadmium resistance; , erythromycin resistance; , mercury resistance; , multidrug resistance to antiseptics and disinfectants; , initiation of plasmid replication. Restriction sites shown: B, II; E, RI.

Citation: Firth N, Skurray R. 2006. Genetics: Accessory Elements and Genetic Exchange, p 413-426. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch33
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Image of FIGURE 4
FIGURE 4

Maps of representative pSK1 family multiresistance plasmids, pSK1 and pSK4 ( ); see text for additional references. Plasmid sizes are indicated on the right. The positions of transposons are indicated above each map. Open and solid boxes denote copies of IS and IS, respectively. Selected loci encoding the following functions are indicated beneath the maps: , aminoglycoside resistance; , penicillin resistance; , trimethoprim resistance; , multidrug resistance to antiseptics and disinfectants; , initiation of plasmid replication. Restriction sites shown: B, II; E, RI.

Citation: Firth N, Skurray R. 2006. Genetics: Accessory Elements and Genetic Exchange, p 413-426. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch33
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Image of FIGURE 5
FIGURE 5

Maps of representative conjugative multiresistance plasmids pSK41, pJE1, pUW3626, pGO1, and pLW1043 ( ); see text for additional references. Plasmid sizes are indicated on the right. The positions of transposons and an integrated copy of the RC plasmid, pUB110, are indicated above each map; the latter and other small cointegrated plasmids are denoted by double lines. Solid boxes denote copies of IS, including the element interrupted by Tn in pLW1043, and open boxes represent truncated copies of IS. Selected loci encoding the following functions are indicated beneath the maps: /, aminoglycoside resistances; , penicillin resistance; , bleomycin resistance; , trimethoprim resistance; , origin of conjugative DNA transfer; , initiation of plasmid replication; , multidrug resistance to antiseptics and disinfectants; , conjugative transfer; , glycopeptide resistance. Restriction sites shown: B, II; E, RI. The position of the II site within IS indicates the orientation of the element.

Citation: Firth N, Skurray R. 2006. Genetics: Accessory Elements and Genetic Exchange, p 413-426. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch33
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Image of FIGURE 6
FIGURE 6

Maps of representative SCC elements ( ). The sizes of the elements are indicated on the right. The positions of transposons Tn and ψTn and cointegrated copies of the RC plasmids pUB110 and pT181 are shown; the plasmids are denoted by double lines. Solid boxes denote copies of IS, and open ovals indicate the position of ψIS, an IS remnant located adjacent to a deletion that removed and part of ). Arrowheads denote TIRs. Non-SCC chromosomal DNA is shown hatched. Selected loci encoding the following functions are indicated: , aminoglycoside resistance; , bleomycin resistance; , cadmium resistance; , recombinases; , MLS resistance; , methicillin resistance; /, regulation of methicillin resistance; , spectinomycin resistance; (K), tetracycline resistance.

Citation: Firth N, Skurray R. 2006. Genetics: Accessory Elements and Genetic Exchange, p 413-426. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch33
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Image of FIGURE 7
FIGURE 7

Maps of representative SaPI elements ( ). The sizes of the elements are indicated on the right. Arrowheads denote left and right directly repeated attachment sequences (attL and attR). Non-SaPI DNA is shown hatched. The position of the transposon-like structure in SaPI-bov2 is shown; the 149-bp direct repeats that bound the structure are denoted as boxes that contain white arrowheads representing IS257-like TIRs. Selected loci encoding the following functions are indicated: bap, biofilm-associated protein; int, integrase; seb, enterotoxin B; sec, enterotoxin C; sec1, enterotoxin C1; sek, enterotoxin K; sel, enterotoxin L; sel′, enterotoxin L remnant; sem, enterotoxin M; sip, staphylococcal integrase protein; ter, phage-like encapsidation terminase; tnp, IS257-like transposase; tst, toxic shock toxin 1.

Citation: Firth N, Skurray R. 2006. Genetics: Accessory Elements and Genetic Exchange, p 413-426. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch33
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Tables

Generic image for table
TABLE 1

Staphylococcal insertion sequences and transposons

See Paulsen et al. ( ), Firth and Skurray ( ), and the text for references.

In the case of IS, association is based on probable involvement in the acquisition, dissemination, and/or expression of the resistance/phenotype.

TIR, terminal inverted repeat. (I), inverted orientation; (D), direct orientation.

C, chromosome; P, plasmid.

ISis also known as IS.

Tn, Tn, and Tnare likely to be similar or identical to Tn.

Tnis likely to be similar or identical to Tn.

Tnand Tnare likely to be similar or identical to Tn.

(I), inverted orientation.

(D), direct orientation.

Citation: Firth N, Skurray R. 2006. Genetics: Accessory Elements and Genetic Exchange, p 413-426. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch33

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