Varieties of Plasmids-ppt

VARIETIES OF PLASMIDS

A MIC 903 TERM PAPER PRESENTATION

BY

SALAM, LATEEF BABATUNDE029071009

DEPARTMENT OF BOTANY AND MICROBIOLOGYUNIVERSITY OF LAGOS

AKOKA, LAGOS, NIGERIA

INTRODUCTION

• Plasmids are self replicative extrachromosomal DNA molecules of finite size that are stably inherited and exchanged promiscuously between a broad spectrum of bacteria and other domains (Perlin, 2002).

• Plasmids allow bacterial (including other domains) populations to ‘sample’ the horizontal gene pool for adaptive traits that might be advantageous for survival under local selective pressure (Sorensen et al., 2005).

• Plasmids also provide genetic variation, acts as sources of recombination and can allow faster gene fixation leading to greater likelihood that the ‘new’ trait will persist (Sorensen et al., 2005).

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INTRODUCTION

• Plasmid classification is generally based on incompatibility group (determined by their replication/partitioning functions) or the genetic information specified by their DNA (Perlin, 2002). Incompatibility grouping had been used to group plasmid of Pseudomonas species (Jacoby, 1977) and the Enterobacteriaceae into 26 incompatibility group (Couturier et al., 1988).

• Most plasmids have a narrow host range allowing only intra-species transfer and replication. However, a small group of plasmids called the broad host range (BHR) plasmids (Inc P, Q, W, N and C) can be transferred and replicated in a wide range of bacteria (Hill and Top, 1998; Dale and Park, 2004). BHR plasmids may either be self-transmissible (Tra+, Mob+) or mobilizable but not self-transmissible (Tra-, Mob+) (Perlin , 2002).

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INTRODUCTION

• Prokaryotes were initially thought to harbour only circular plasmids. However with the discovery of double stranded linear plasmids in the spirochaete that cause lyme disease, Borrelia borgdorferi (Barbour and Garon, 1987), linear plasmids have also been detected in the genera Streptomyces (Kinashi et al., 1994), Mycobacterium (Le Dantec et al., 2001), Rhodococcus (Larkin et al., 2005) and Arthrobacter (Overhage et al., 2005).

VARIETIES OF PLASMIDS BASED ON STRUCTURE

• Linear DNA plasmids structure are of two types: those having covalently closed hairpin loops at both termini with no exposed 5’ or 3’ends anywhere in the molecule (Borrelia plasmids, poxviruses, Rhizoctonia solani); and those having terminal inverted repeats (TIRs) at both ends and a protein covalently bound at their 5’-end (actinomycetes plasmids, mitochondrial plasmids of filamentous fungi, adenovirus) (Salas, 1991; del Solar, 1998)

• Linear plasmids of the first group (Borrelia plasmids) replicate via concatemeric intermediates (Salas, 1991). Linear plasmids of the second group replicate by protein priming mechanism ( bacteriophage φ29) (Salas, 1991) or bidirectional replication initiated from an internal position in the DNA molecule (Streptomyces) (Chang and Cohen, 1994).


Figure 1: Mode of replication of linear plasmids in Borrelia (Dale and Park, 2004)


Figure 2: Mode of replication of linear plasmids in Streptomyces. TP, terminal protein (Dale and Park, 2004).

VARIETIES OF PLASMIDS BASED ON STRUCTURE• Circular plasmids have been reported in filamentous fungi such as

Neurospora species and Absidia glauca (Griffiths, 1995), Gram positive and Gram negative bacteria, 2µm plasmid in yeast and rDNA plasmids in unicellular eukaryotes (Perlin, 2002).

• Three general replication mechanisms for circular plasmids have been reported. They include theta (θ) type (e.g. ColE1, R6K, ColE2-like plasmids), rolling circle (e.g. Staphylococcal plasmids: pT181, pC221, pC194; Streptococcal plasmids: pMV158, pLS1) and strand displacement (e.g. IncQ plasmids: RSF110, R1162, R300B) (Novick, 1989; Thomas et al., 1990; del Solar et al., 1998; Rawling and Tietze, 2001).


Figure 3: genetic map of ColE1 circular plasmid: colE1, imm: genes for production of, and immunity to colicin E1; mob codes for nuclease required for mobilization; rom codes for protein required for effective control of copy number; oriT: origin of conjugal transfer; oriV: origin of replication (Dale and Park, 2004).


Figure 4: Model for rolling circle replication (del Solar et al., 1998)

VARIETIES OF PLASMIDS BASED ON FUNCTIONS

Resistance plasmids• The role of plasmids in evolution of bacterial genome and adaptation

to specific environmental changes has contributed immensely to the emergence of antibiotic and heavy metal resistance plasmids.

• This feat is aided by the activities of transposons, which promote the movement of resistance genes between plasmids or from the chromosome of naturally resistant organisms onto a plasmid ( Dale and Park, 2004; Kapil, 2005).

• Bacteria can be resistant to various antibiotics either by acquisition of several independent plasmids or through acquiring a single plasmid with many resistance determinant on it (Hill and Top, 1998).

• The mechanism of plasmid mediated heavy metal resistance are efflux


pumping of the toxic metal out of the bacterial cell, bioaccumulation in physiologically inaccessible compound and redox chemistry in which a more toxic ion species is converted to a less toxic ion (Endo et al., 2002)

• Plasmid-mediated mercury (mer) (Silver and Walderhaug, 1994), arsenic (ars) (Wu and Rosen, 1993), cadmium (Cad) (Tsai et al., 1993), and chromate (Chr) (Pimentel et al., 2002) resistance have been reported for Gram positive and Gram negative with various mechanisms of resistance.


Table 1: some antibiotic resistance plasmids, their incompatibility groups and phenotypes

Abbreviations used: Km, kanamycin; Tc, tetracycline; Ap, ampicillin; Sm, streptomycin; Sp, spectinomycin; Cm, chloramphenicol, Tp, trimethoprim; BHR, broad host range (Hill and Top, 1998)


Bacteriocin-encoded plasmids• Bacteriocin are compounds produced by bacteria to kill other bacteria.

Each type of bacteriocin is named according to the bacteria of origin. Colicins are the best studied bacteriocins (Davies and Reeves, 1975) and are encoded on conjugative plasmids or small multicopy non-conjugative plasmids (Moat et al., 2002).

• Different colicins have different mechanisms of action. Colicin E1 and K uncouple energy-dependent processes in the cytoplasmic membrane; colicin E2 causes inhibition of cell division and DNA degradation; and colicin E3 prevent protein synthesis by cleavage of the 16S rRNA (Perlin, 2002).

VARIETIES OF PLASMIDS BASED ON FUNCTIONSVirulence plasmids• Virulence plasmids of Salmonella (50-90-kb in size) have an spv (7.8-

kb) region that confers virulent phenotype on its host (Rotger and Casadesus, 1999).

• Mycobacterium ulcerans harbour a 174-kb plasmid pMUM001 that contain a cluster of genes encoding very large polyketide synthases and polyketide-modifying enzymes, which are necessary for mycolactone synthesis (Stinear et al., 2004). Mycolactone is a macrolide with a cytotoxic, analgesic, and immunosuppressive activities and thus play a key role in pathogenesis (George et al., 1999).

• E. coli harbours an enterotoxin-producing plasmid and a plasmid that encode the pili K88 antigen. Both plasmids are required for pathogenicity (Perlin, 2002).

VARIETIES OF PLASMIDS BASED ON FUNCTIONSPhytopathogenic plasmids• Virulent strains of Agrobacterium tumefaciens harbours a 200-kb

tumour-inducing (Ti) plasmids that causes crown gall tumour on most dicotyledonous plants when it infect wounded plant tissue (DeCleene and DeLey, 1976).

• Specific segment of Ti plasmid, the T-DNA that encodes enzymes for biosynthesis of plant growth hormones enters plant cells and stably integrate into plant nuclear DNA (Chilton et al., 1980) causing transformed cells to grow as crown gall tumours (Zhu et al., 2000).

• Other phytopathogenic plasmids include Ri-plasmid of Agrobacterium rhizogenes (hairy root disease of dicotyledonous plants), 82-kb plasmid of Pseudomonas syringae pv. Eriobotryae (stem canker of loquat) etc (Kamiunten, 1995; Gelvin, 2003).

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VARIETIES OF PLASMIDS BASED ON FUNCTIONSCatabolic plasmids• The first reported catabolic plasmid was the CAM plasmid of

Pseudomonas putida that controlled the oxidation of naturally occurring terpene, camphor (Rheinwald et al., 1973).

• Catabolic plasmids are characterized by their large size. Cho and Kim (2001) isolated a catabolic plasmid pKS14 (>500-kb) from Sphingomonas sp. strain KS14 responsible for the degradation of phenanthrene and pyrene. The genomic sequence of Rhodococcus sp. strain RHA1 revealed three large linear catabolic plasmids: pRHL1 (1100-kb), pRHL2 (450-kb) and pRHL3 (330-kb) (Larkin et al., 2005).

• Degradation of naturally occurring compounds is mostly encoded by IncP-2 and IncP-9 catabolic plasmids. However, degradation of xenobiotics is often encoded by the BHR IncP-1 plasmids (Top et al., 2000).

VARIETIES OF PLASMIDS BASED ON FUNCTIONSConjugative plasmids• Conjugation involves direct cell-to-cell contact, mating-pair formation

and DNA exchange mediated by conjugative pili (Sorensen et al., 2005).

• Conjugative plasmids are plasmids that encode all necessary gene products, which enable the potential donor cell to carry out a specific contact cycle with the recipient cell (Perlin, 2002).

• An E. coli plasmid, F-factor DNA (100-kb) was the first reported conjugative plasmid with genes coding for autonomous replication, sex pili formation, and conjugal transfer functions along with several insertion sequences at various sites (Moat et al., 2002).

• Many Gram positive species also possess plasmids that are transmissible by conjugation using similar mechanism with Gram nega


negative bacteria but with modification ranging from absence of genes for pilus formation and lack of conjugative relaxase in Streptomyces to pheromone-inducing expression of transfer (tra) genes of specific plasmid in the donor cell by Enterococcus (Grohmann et al., 2003).

• Examples of conjugative plasmids are the broad host range plasmids (IncP, Q, W, N, and C), ColE1, F plasmids.


Figure 5: Genetic map of Escherichia coli F factor showing the four major regions: The inc, rep region determines replication and plasmid incompatibility properties; the tra region provides conjugative DNA mobilization functions; the region containing the four transposable elements that facilitates interaction between F factor and other DNA molecules; and the silent region (Porter, 2002).


Sex pheromone plasmids• Pheromones are secreted chemicals used for signalling between two

or more individuals. Pheromone conjugative plasmids are confined to the Enterococci and encode antibiotic resistance, bacteriocins and hemolysins (Grohmann et al., 2003).

• In this novel transfer system, recipient cells secrete a family of heat stable peptide pheromones with specificities for donor carrying various conjugative plasmid that trigger response from donor bacteria harbouring a particular plasmid, which synthesize an adhesin that facilitates the formation of mating aggregate with nearby recipients (Dale and Park, 2004).

• Examples of sex pheromone plasmids are pAD1 (59.3-kb, hemolysin/bacteriocin plasmid), and pCF10 (65-kb, tetracycline resistance) (Grohmann et al., 2003).

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Senescence plasmids in fungi• Senescence is an inherent degenerative program in multicellular

organisms that is manifested by a progressive decline in cellular energy production culminating in the death of a part or the whole organism (D’souza and Maheshwari, 2002).

• This phenomenon was found to be associated with the accumulation of high copy number circular plasmids (sen DNAs) in the mitochondrial respiration resulting in the death of the fungus (D’souza and Maheshwari, 2002).

• Mitochondrial-based linear plasmids from Neurospora sp. were also found to be responsible for the death of the strains harbouring them by insertion of their DNA into the mitochondrial genome resulting in disruption of several genes leading to senescence and death due to defective respiration (Bertrand, 2000; Griffiths, 1998).

CONCLUSIONThe world of plasmid is a world of unending possibilities. The unparalleled catabolic versatility, virulence and pathogenicity coupled with resistances to antibiotics and heavy metals that is often encoded by plasmids and promiscously exchanged and transferred during horizontal gene transfer make plasmid biology an interesting field of research and the cornerstone of genetic engineering.

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Varieties of Plasmids-ppt