Varieties of Plasmids-ppt

VARIETIES OF PLASMIDS A MIC 903 TERM PAPER PRESENTATION BY SALAM, LATEEF BABATUNDE 029071009 DEPARTMENT DEPARTMENT OF BOT BO TANY AND MICROBIO MICR OBIOLOGY LOGY UNIVERSITY OF LAGOS AKOKA, LAGOS, NIGERIA

INTRODUCTION 

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Plasmids are self replicative extrachromosomal DNA molecules of  finit finitee size size that that are are stab stably ly inher inherit ited ed and and exch exchan ange ged d prom promis iscu cuous ously ly   bet betwe ween en a broa broad d spec spectr trum um of bact bacter eria ia and and othe otherr doma domain inss (Per (Perli lin, n, 2002). Plasmi Plasmids ds allow allow bacteri bacterial al (incl (includi uding ng other other domai domains) ns) populati populations ons to µsample¶ 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 likelihood that the the µnew¶ µnew¶ trait will persist persist (Sorensen (Sorensen et al ., ., 2005).

INTRODUCTION 

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Plasmi Plasmid d classi classific ficati ation on is general generally ly based based on incomp incompati atibil bility ity group group (determined by their replication/partitioning functions) or the genetic information specified by their DNA (Perlin, 2002). Incompatibility grou groupi ping ng had had been used used to group group plas plasmi mid d of  Pseudomona Pseudomona s  s species (Jacob (Jacoby y, 1977) 1977) and the the Entero Enterobac bacte teria riacea ceaee into into 26 incomp incompati atibil bility ity group (Couturier et (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 1998;; Dal Dale and Park, ark, 2004 2004). ). BHR BHR plas plasm mids ids may eith either er be sel selftransmissible (Tra +, Mob+) or mobilizable but not self-transmissible (Tra-, Mob+) (Perlin , 2002).

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 Streptomyce s Streptomyce s (Kinashi et al ., . , 1994 1994), ), Mycobacterium (Le Dantec et al ., 2001) 001),, Rhodococcu s Rhodococcu s (Larkin et al ., 2005) and  Arthrobacter (Overhage  Arthrobacter (Overhage et al ., ., 2005).

VARIETIES OF PLASMIDS PLASMID S BASED ON STRUCTURE STRU CTURE 

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Line inear DNA DNA plas plasm mids ids stru struct ctur uree are are of two two type types: s: thos thosee havi havin ng covalently closed hairpin loops at both termini with no exposed 5¶ or  3¶en 3¶ends ds any anywher wheree in the the molec olecul ulee ( Borrelia plasmids, plasmids, poxviruses poxviruses,,  Rhizoctonia solani); olani); and those having terminal inverted repeats (TIRs) at both ends and a protein covalently bound at their 5¶-end (act (actin inom omyc ycet etes es plas plasmi mids ds,, mito mitocho chondr ndria iall plas plasmi mids ds of fila filame ment ntou ouss fungi, adenovirus) (Salas, 1991; del Solar, 1998) Linear plasmids of the first group ( Borrelia plasmids) replicate via conc concat atem emer eric ic inte interm rmed edia iate tess (Sal (Salas, as, 1991) 1991).. Line Linear ar plas plasmi mids ds of the the second group replicate by protein priming mechanism ( bacteriophage 29) 29) (Sal (Salas as,, 1991 1991)) or bidi bidire rect ctio iona nall repl repliicati cation on init initiiated ated fr from om an internal position in the DNA molecule (Streptomyce ( Streptomyce s  s)) (Chang and Cohen, 1994).

VARIETIES OF PLASMIDS PLASMID S BASED ON STRUCTURE STRU CTURE

Figure

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

VARI ARIETIE ETIES S OF PLAS LASMIDS IDS BAS BASED ON STRUC TRUCTU TURE RE

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

VARI ARIETIE ETIES S OF PLAS LASMIDS IDS BAS BASED ON STRUC TRUCTU TURE RE 

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Circular plasmids have been reported in filamentous fungi such as euro s pora spec specie iess and and Ab s Ab sid idia ia glau glauca ca (Gri (Grifffiths fiths,, 1995) 1995),, Gram Gram  N euro s  positive  positive and Gram Gram negative negative bacteria, bacteria, 2 m plasmid plasmid in yeast and rDNA  plasmids in unicellular eukaryotes (Perlin, 2002). Three general replication mechanisms for circular plasmids have been reported. They include theta () type (e.g. ColE1, R6K, ColE2-like  plasmids), rolli (e.g.. Stap Staphy hylo lococ coccal cal plasm plasmid ids: s: pT18 pT181, 1, olling ng cir circle cle (e.g  pC221, pC194; Streptococcal plasmids: p MV158, pLS1) and strand 110, R1162, R1162, R300B) (Novick, displacement (e.g. IncQ plasmids: RS F110, 1989; Thomas et al ., ., 1990; del Solar et Solar  et al ., ., 1998; Rawling and Tietze, 2001).

VARIETIES OF PLASMIDS BASED ON STRUCTURE

Figure

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

VARI ARIETI ETIES OF PLAS PLASMI MIDS DS BASE BASED D ON STRU STRUCT CTUR URE E

Figure

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

VARIETIES OF PLASMIDS PLASMID S BASED ON FUNCTIONS FUN CTIONS esistance plasmids R esistance 

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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 movem vement of resi esistance genes between pla 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 d eterminant on it (Hill and Top, Top, 1998). The mechanism of plasmid mediated heavy metal resistance are efflux

VARIETIES OF PLASMIDS PLASMID S BASED ON FUNCTIONS FUN CTIONS  pumping of the toxic metal out of the bacterial cell, bioaccumulation in physio physiolog logica ically lly inacces inaccessi sible ble compou compound nd and redox redox chemi chemistr stry y in which a more toxic ion species is converted to a less toxic ion (Endo et al ., ., 2002) 

Plasmi Plasmid-m d-medi ediat ated ed mercury mercury (mer ) (Sil (Silver ver and and Walder alderha haug ug,, 1994) 1994),, arsenic (ar  (ar  s) ( C ad  ad ) (Tsai (Tsai et al ., .,  s) (Wu and Rosen, 1993), cadmium (C  1993), and chromate (C  ( C hr  ., 2002) resistance have hr ) (Pimentel et al .,   bee been n repo report rted ed for for Gram Gram posi positi tive ve and and Gram Gram nega negati tive ve with with vari variou ouss mechanisms of resistance.

VARIETIES OF PLASMIDS PLASMID S BASED ON FUNCTIONS FUN CTIONS Tabl able 1: som some antib ntibio ioti ticc resi resist stan ance ce plas plasm mids, ids, thei their  r  incompatibility groups and phenotypes

Abbrevia Abbreviation tionss used: Km, Km, kanamyci kanamycin; n; Tc, tetrac tetracyc ycline line;; Ap, ampici ampicilli llin; n; Sm, streptom streptomyci ycin; n; Sp, spectino spectinomyc mycin; in; Cm, chloramp chloramphenic henicol, ol, Tp, trimet trimethopri hoprim; m; BHR, broad host range (Hill and Top, 1998)

VARIETIES OF PLASMIDS PLASMID S BASED ON FUNCTIONS FUN CTIONS Bacteriocin-encoded plasmids 

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Bacteriocin are compounds produced by bacteria to kill other bacteria. Each type of bacterioci bacteriocin n is named according according to the bacteria bacteria of origin. origin. Colicins are the best studied bacteriocins (Davies and Reeves, 1975) and are encoded on conjugative plasmids or small multicopy nonconjugative plasmids ( Moat et al ., ., 2002). Different colicins have different mechanisms of action. Colicin E1 and K unco ncouple ple energ ergy-depend pendeent pro processes in the cytopl oplasmic membrane; colicin E2 causes inhibition of cell division and DNA degradation; and colicin E3 prevent protein synthesis by cleavage of  the 16S rRNA rRNA (Perlin, (Perlin, 2002). 2002).

VARIETIES OF PLASMIDS PLASMID S BASED ON FUNCTIONS FUN CTIONS Virulence plasmids 

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Virulence

plasmids of Salmonella (50-90-kb in size) have an spv (7.8kb) region that confers virulent phenotype on its host (Rotger and Casadesus, 1999). Mycobacterium ulceran s ulceran s harbour a 174-kb plasmid p MUM001 that contain a cluster of genes encoding very large polyketide synthases and poly olyket ketide-m e-modif difying enz enzymes, which are neces cessary ary for  mycol mycolact actone one synthe synthesis sis (Stine (Stinear  ar  et al ., . , 2004 2004). ). Mycol colact actone is a macr macrol oliide with with a cyto cytoto toxi xic, c, anal analge gesi sic, c, and and immu immuno nosu supp pprressi essive ve activities and thus play a key role in pathogenesis (George et al ., ., 1999). E. coli harbours an enterotoxin-producing plasmid and a plasmid that encod code the pil pili K88 antigen. Both oth plas plasm mids are requir uired for   pathogenicity (Perlin, 2002).

VARIETIES OF PLASMIDS PLASMID S BASED ON FUNCTIONS FUN CTIONS Phytopathogenic plasmids 

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irulen entt Virul

stra strain inss of  Agrobacterium Agrobacterium tumefacien s harb harbour ourss a 200200-kb 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 inte integr grat atee into into plant plant nucl nuclea earr DNA DNA (Chi (Chilt lton on et al ., . , 1980 1980)) caus causin ing g transformed cells to grow as crown gall tumours (Zhu et al ., ., 2000). Other phytopathogenic plasmids include Ri-plasmid of  Agrobacterium rhizogene s (hai (hairy ry root root dise diseas asee of dico dicoty tyle ledo dono nous us plan plants ts), ), 8282-kb   plasmid of Ps of  Pseudomona eudomona s pv. Eriobotryae (stem canker of   s s yringae pv. loquat) etc (Kamiunten, 1995; Gelvin, 2003).

VARIETIES OF PLASMIDS BASED ON FUNCTIONS Catabolic plasmids 

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The firs firstt repo report rted ed catab atabol oliic plas plasm mid was was the CAM plas plasmi mid d of  that cont contro roll lled ed the the oxid oxidat atiion of natu naturrally ally  Pseudomona  Pseudomona s  s putida that 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 Sphingomona s Sphingomona s sp. sp. stra strain in KS14 KS14 resp respons onsib ible le for for the the degr degrad adat atio ion n of   phenanthr  phenanthrene ene and pyrene. pyrene. The genomic genomic sequence sequence of Rhodococcu of Rhodococcu s  s sp. strain RHA1 revealed three large linear catabolic plasmids: pRHL1 (110 (1100-k 0-kb) b),, pRHL2 pRHL2 (450(450-kb kb)) and pRHL pRHL3 3 (330 (330-k -kb) b) (Lar (Larki kin n et al ., ., 2005). Degradation of naturally occurring compounds is mostly encoded by IncP IncP-2 -2 and and IncP IncP-9 -9 cata catabo boli licc plas plasmi mids ds.. Howe Howeve verr, degr degrad adat atio ion n of  xenobiotics is often encoded by the BHR IncP-1 plasmids (Top et al ., .,

VARIETIES OF PLASMIDS BASED ON FUNCTIONS Conjugative plasmids 

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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 transm transmiss issibl iblee by conjuga conjugati tion on using using simila similarr mechan mechanism ism with with Gram Gram

VARIETIES OF PLASMIDS BASED ON FUNCTIONS negative bacteria but with modification ranging from absence of genes for pilus formation and lack of conjugative c onjugative relaxase in Streptomyce s Streptomyce s to   pherom pheromone one-in -induc ducing ing expres expressio sion n of transfe transferr (tra) tra) genes of specific  plasmid in the donor cell by Enterococcu s (Grohmann et al ., ., 2003). 

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

VARIETIES OF PLASMIDS PLASMID S BASED ON FUNCTIONS FUN CTIONS

5: Genetic map of E  of  E  scherichia  scherichia coli F factor showing the four major regions: The inc, inc, rep region determines replication and plasmid incompatibility properties; the tra region region provi provides des conjug conjugat ativ ivee DNA mobil mobiliz izati ation on funct functio ions; ns; the regio region n containing the four transposable elements that facilitates interaction between F factor and other DNA molecules; molecules; and the silent region (Porter, (Porter, 2002). Figure

VARIETIES OF PLASMIDS BASED ON FUNCTIONS Sex pheromone plasmids 

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Pheromones are secreted chemicals used for signalling between two or  more individuals. Pheromone conjugative plasmids are confined to the Ente Enterrococ ococci ci and and enco encode de anti antibi biot otic ic resi resist stan ance ce,, bact bacter erio ioci cins ns and and hemolysins (Grohmann et al ., ., 2003). In this novel transfer system, recipient cells secrete a family of heat stab stable le pept peptid idee pher pherom omon ones es with with spec specif ific icit itie iess for for dono donorr carr carry ying ing various conjugative plasmid that trigger response from donor bacteria harbou harbourin ring g a parti particul cular ar plasmi plasmid, d, which which synth synthesi esize ze an adhesi adhesin n that that facilitates the formation of mating aggregate with nearby recipients (Dale and Park, 2004). Examples of sex pheromone plasmids are pAD1 (59.3-kb, hemoly hemolysi sin/ n/ba bact cter erio ioci cin n plas plasmi mid) d),, and and pCF10 (65(65-kb kb,, tetr tetrac acy yclin clinee resistance) (Grohmann et al ., ., 2003).

VARIETIES OF PLASMIDS BASED ON FUNCTIONS Senescence plasmids in fungi 

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Sene Senesc scen ence ce is an inhe inhere rent nt dege degene nera rati tive ve prog progra ram m in mult multic icel ellu lula lar  r  orga organi nism smss that that is mani manife fest sted ed by a progr progres essi sive ve decl declin inee in cell cellul ular  ar  energy production culminating in the death of a part or the whole organism (D¶souza (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 (D¶souza and Maheshwari, 2002). Mitochondrial-based

linear plasmids from N euro s euro s pora 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).

CONCLUSION The worl orld of plasmid is a worl orld of unen nending poss ossibil bilities. 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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