Replication of plasmids
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Summary One of the characteristics that differentiates plasmids from other extrachromosomal genetic elements, transposons and viruses, is the controlled replication that allows stable inheritance in dividing cells. At the same time, the mechanism of replication of some plasmids is very similar to that of some viruses, and indeed some plasmids might have viral origin. In the case of other plasmids, their replication mechanism is similar to that used by the host. On the one hand, therefore, the study of plasmid replication may give hints as to the origin of a particular group of these extrachromosomal elements. On the other, the research on replication of plasmids helped to solve basic questions pertaining to this basic molecular process in general. The first basic problem of any process of DNA replication is that of priming, since none of the replicative polymerases can start DNA synthesis using just free nucleotides. Plasmids use three strategies to solve this problem. Some linear plasmids code for a replication protein which provides an OH group to which the first nucleotide of the copy molecule can be attached by a plasmid-coded DNA polymerase. Another strategy is to bring the host primase to the origin of replication. This enzyme synthesizes a short RNA molecule the 3'OH end of which can be elongated by the DNA polymerase of the host. The mechanism of replication of such plasmids shows many similarities to that of the host chromosome. Some plasmids, it may be added, code for their own primase. Finally, at the origin of replication of other plasmids, for instance those replicating using the rolling-cycle mechanism, one of the parent DNA strands becomes cleaved to provide a free 3'OH group. Research on plasmid replication provided many answers not only to basic questions on replication in general: it was also very important for understanding the mechanisms of gene regulation. Plasmid replication needs to be controlled so that the metabolic burden on the host is not excessive. There are two known mechanisms used to control the replication of bacterial plasmids. In one, the role of a regulator is played, actually, by the plasmid DNA sequences in the origin region. This is the mechanism of plasmid handcuffing, named after the appearance of two plasmid molecules brought together when such regions from two plasmids interact indirectly, the mechanism by which replication is repressed. As the interaction is reversible, when plasmid concentration in the growing and dividing cell drops, the molecules can separate and replicate. In a different mechanism of replication regulation, the role of the regulator is played by small molecules (RNA, and sometimes also a protein) the concentration of which depends on plasmid copy number and which inhibit the synthesis of another molecule coded for a plasmid (usually a protein, sometimes RNA) that is important for replication initiation. Indeed, it was thanks to the research on regulation of plasmid replication that the mechanism of regulation by small RNA molecules (antisense RNA) has been first described in detail. The reason for such a historical importance of research on plasmid replication is that it is easier to achieve the genetic modification of plasmids than modification of the host genome. Moreover, the effects of a modification of an element which is not necessary for survival of the cell can be observed and interpreted with less difficulty. For the same reasons of easy manipulation, introduction of artificial plasmids into the cells is the main method of genetic modification. Such molecules may not be replicative in the target host, and thus either are eliminated from the cells with time, or integrate into the host chromosomes. In the case of a majority of biotechnological applications, however, the plasmids used are replicative, and therefore it is important to be able to control their copy level in the cells. Replicative elements are being also considered for use in therapy. Thus, the research on plasmid replication remains of vital importance.
- ARAGONOZA M. T., MIN J., HU Z., AKINS R. A., 1994. Distribution of seven homology groups of mitochondrial plasmids in Neurospora: evidence for widespread mobility between species in nature. Curr. Genet. 26, 62-73.
- ATLUNG T., CHRISTENSEN B. B., HANSEN F. G. , 1999. Role of the Rom protein in copy number control of plasmid pBR322 at different growth rates in Escherichia coli K-12. Plasmid 41, 110-119.
- BAO K., COHEN S. N., 2001. Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces. Genes. Dev. 15, 1518-1527.
- BELNAP D. M., OLSON N. H, CLADEL N. M, NEWCOMB W. W., BROWN J.C., KREIDER J. W., CHRISTENSEN N. D., BAKER T. S., 1996. Conserverd features in papillomavirus and polyomavirus capsids. J. Mol. Biol. 259, 249-263.
- BLAISONNEAU J., SOR F., CHERET G., YARROW D., FUKUHARA H., 1997. A circular plasmid fromt the yeast Torulaspora delbrueckii. Plasmid 38, 202-209.
- BLAISONNEAU J., NOSEK J., FUKUHARA H., 1999. Linear DNA plasmid pPK2 of Pichia kluyveri: distinction between cytoplasmic and mitochondrial linear plasmids in yeast.Yeast 15, 781-791.
- BROWN W R., MEE P. J., SHEN M. H., 2000. Artificial chromosomes: ideal vectors? Trends Biotech. 18, 218-223.
- CAMENISCH G., GRUBER M., DONOHO G., VAN SLOUN P., WENGER R. H., GASSMANN M., 1996. A polyoma-based episomal vector efficiently expresses exogenous genes in mouse embryonic stem cells. Nucleic Acids Res. 24, 3707-3713.
- CASJENS S., 1999. Evolution of the linear DNA replicons of the Borrelia spirochetes. Curr. Opin. Microbiol. 5, 529-534.
- CHATTORAJ, D. K., 2000. Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37, 467-476.
- COLLINS R. A., SAVILLE B. J., 1990. Independent transfer of mitochondrial chromosomes and plasmids during unstable vegetative fusion in Neurospora. Nature 345, 177-179.
- CRAENENBROECKK., VANHOENACKER P., HAEGEMAN G., 2000. Episomal vectors for gene expression in mammalian cells. Eur. J. Biochem. 267, 5665-5678.
- DARQUET A. -M., CAMERON B., WILS P., SHERMAN D., CROUZET J., 1997. A new DNA vehicle for nonviral gene delivery: supercoiled minicirlce. Gene Therapy 4, 1341-1349.
- VAN DER SOLAR G., ESPINOSA M., 2000. Plasmid copy number control: a never growing story. Mol. Microbiol. 37, 492-500.
- VAN DER SOLAR, G., GIRALDO R., RUIZ-ECHEVARRIA M.J., ESPINOSA M., DIAZ-OREJAS R., 1998. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62, 434-464.
- VAN DER SOLAR, G. ALONSO J.C, ESPINOSA M., DIAZ-OREJAS R., 1996. Broad-hoast range plasmid replication: an open question. Mol. Microbiol. 21, 661-666.
- DHAR S. K., CHOUDHURY N. R., MITTAL V., BHATTA CHARYAA., BHATTACHARYAS., 1996. Replication initiates at multiple dispersed sites in the ribosomal DNA plasmid of the protozoan parasite Entamaeba histolytica. Mol. Cell. Biol. 16, 2314-2324.
- FARRAR, N. A., WILLIAMS K L., 1988. Nuclear plasmids in the simple eukaryotes Saccharomyces cerevisiae and Dictyostelium discoideum. Trends Genet. 4, 343-348.
- FUKUHARA H., 1995. Linear DNA plasmids of yeast. FEMS Microbiol. Lett. 131, 1-9.
- GIBBS M. J., KOGA R., MORIYAMA H., PFEIFFER P., FUKUHARA T., 2000. Phylogenetic analysis of some large double-stranded RNA replicons from plants suggests they evolved from a defective single-stranded RNA virus. J. Gen. Virol. 81, 227-233.
- GONZALES C. M., SPENCER T. D., PENDLEY S. S, WELKER D. L., 1999. Dgp1 and Dfp1 are closely related plasmids in the Dictyostelium Ddp2 plasmid family. Plasmid 41, 89-96.
- GRIFFITHS A. J., KRAUS S. R., BARON R., COURT D. A., MYERS C. J., BERTRAND H. 1990. Heterokaryotic transmission of senescence plasmid DNA in Neuospora. Curr. Genet. 21, 479-484.
- GRIFFITHS A. J., 1995. Natural plasmids of filamentous fungi. Microbiol. Rev. 59, 673-685.
- HARTIKKA J., SAWDEY M., CORNEFERT-JENSEN F., MARGALITH M., BARNHART K., NOLASCO M., VAHLSING H. L., MEEK J., MARQUET M., HOBART P., NORMAN J., MANTHORPE M., 1996. An improved plasmid DNA expression vector for direct injection into skeletal muscle. Hum. Gene Ther. 7, 1205-1217
- HINNEBUSCH J., TILLY K., 1993. Linear plasmids and chromosomes in bacteria. Mol. Microbiology 10, 917-922.
- HOCHHUT B., MARRERO J., WALDOR M. K., 2000. Mobilization of plasmids and chromosomal DNA mediated by the SXT element, a constin found in Vibrio cholerae O139. J. Bacteriol. 182, 2043-2047.
- HONDA Y., SAKAI H., HIASA H., TANAKA K., KOMANO T., B AGDASARIAN M., 1991. Functional division and reconstruction of a plasmid replication origin: molecular dissection of the oriV of the broad-host-range plasmid RSF1010. Proc. Natl. Acad. Sci. USA 88, 179-183.
- HUBER D. H., RUSTCHENKO E., 2001. Large circular and linear rDNA plasmids in Candida albicans. Yeast 18, 261-271.
- JACHYMCZYK W., 1995. Replikacja DNA. [W:] Genetyka molekulanra. WĘGLEŃSKI P. (red.) Wydawnictwo Naukowe PWN, Warszawa, 59-105.
- KEMPKEN F., HERMANNS J., OSIEWACZ H. D., 1992. Evolution of linear plasmids. J. Mol. Evol. 35, 502-513.
- KHAN S. A., 2000. Plasmid rolling-circle replication: recent developments. Mol. Microbiol. 37, 477-484.
- KOLSTO A. -B., 1997. Dynamic bacterial genome organization. Mol. Microbiol. 24, 241-248.
- LANKA E., WILKINS B. M., 1995. DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 64, 141-169.
- LEITING B., LINDNER I. J., NOEGEL A. A.,1990. The extrachromosomal replication of Dictyostelium discoideum plasmid Dpd2 requires a cis-acting element and a plasmid-encoded trans-acting factor. Mol. Cell. Biol. 7, 3727-3736.
- LLOSA M., GOMIS-RÜTH F. X., COLL M., CRUZ F. (2002) Bacterial conjugation: a two-step mechanism for DNA transport. Mol. Microbiol. 45, 1-8.
- LUDWIG D. L, BRUSCHI C. V., 1991. The 2m plasmid as a nonselectable, stable, high copy number yeast vector. Plasmid 25, 81-95.
- MEINHARDT F., KEMPKEN F., KAMPER J., ESSER K., 1990. Linear plasmids among eukaryotes: fundamentals and application. Curr. Genet. 17, 89-95.
- MEINHARDT F., SCHAFFRATH R., LARSEN M., 1997. Microbial linear plasmids. Appl. Microbiol. Biotechnol. 47, 329-336.
- MIYASHITA S., HIROCHIKA H., IKEDA J. E. HASHIBA T., 1990. Linear plasmid DNAs of the plant pathogenic fungus Rhizoctonia solani with unique terminal structures. Mol. Gen. Genet. 220, 165-171.
- MORIYAMA H., NITTA T., FUKUHARA T., 1995. Double-stranded RNA in rice: a novel RNA replicon in plants. Mol. Gen. Genet. 248, 364-369.
- NOMURA N., MASAI H., INUZUKA M., MIYAZAKI C., OHTSUBO E., ITOH T., SASAMOTO S., MATSUI M., ISHIZAKI R., ARAI K., 1991. Identification of eleven single-strand initiation sequences (ssi) for priming of DNA replication in the F, R6K, R100 and ColE2 plasmids. Gene 108, 15-22.
- PETES T. D., WILLIAMSON D. H., 1994. A novel structural form of the 2 micron plasmid of the yeast Saccharomyces cerevisiae. Yeast 10, 1341-1345.
- RASOOLY, A. R., RASOOLY, R. S., 1997. How rolling circle plasmids control their copy number. Trends Microbiol. 5, 440-446.
- RIEBEN W. K., GONZALES C. M., GONZALES S. T., PILKINGTON K. J., KIYOSAWA H., HUGHES J.E., WELKER D. L., 1998. Dictyostelium discoideum nuclear plasmid Ddp5 is a chimera related to the Ddp1 and Ddp2 plasmid families. Genetics 148, 1117-1125.
- RODIRUGEZ-COUSINO N., SOLORZANO A., FUJIMURA T, ESTEBAN R., 1998. Yeast positive - stranded virus-like RNA replicons, 20S and 23S RNA terminal nucleotide sequences and 3'end secondary structures resemble those of RNA coliphages. J. Biol. Chem. 273, 20363-20371.
- ROTHSTEIN R., GANGLOFF S., 1999. The shuffling of a mortal coil. Nat. Genetics 22, 4-6.
- SALYERS A. A., SHOEMAKER N.B., STEVENS A M., LI L.-Y., 1995. Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol. Rev. 59, 579-590.
- VAN DER SAND S. T. , GREENHALF W., GARDNER D. C., OLIVER S. G., 1995. The maintenance of self-replicating plasmids in Saccharomyces cerevisiae: mathematical modelling, computer simulations and experimental tests. Yeast 11, 641-658.
- SHADAN F. F., VILLARREAL L. P., 1993. Coevolution of persistetly infecting small DNA viruses and their hosts linked to host-interactive regulatory domains. Proc. Natl. Acad. Sci. USA 90, 4117-4121.
- SEEGERS J. F., ZHAO A. C., MEIJER W. J., KHAN S. A., VENEMA G., BRON S., 1995. Structural and functional analysis of the single-strand origin of replication from the lactococcal plasmid pWV01. Mol. Gen. Genet. 249, 43-50.
- SHAMMAT I. M., GONZALES C. M., WELKER D. L., 1998. Dictyostelium discoideum nuclear plasmid Dpd6 is a new member of the Dpd2 family. Curr. Genet. 33, 77-82.
- SINCLAIR D., MILLS K., GUARENTE L., 1998. Aging in Saccharomyces cerevisiae. Annu. Rev. Microbiol. 52, 533-560.
- TAKECHI S., ITOH T., 1995. Initiation of unidirectional ColE2 DNA replication by a unique priming mechanism. Nucl. Acids Res. 23, 4196-41201.
- VOLFF J. -N., ALTEMBUCHNER J., 2000. A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol. Lett. 186, 143-150.
- VOS J. M., 1999 Therapeutic mammalian artificial episomal chromosomes. Curr. Opin. Mol. Ther. 1, 204-215.
- WADE-MARTINS R., WHITE R. E., KIMURA H., COOK P. R., JAMES M.R., 2000. Stable correction of a genetic deficiency in human cells by an episome carrying a 115 kb genomic transgene. Nat. Biotechnol. 18, 1311-1314.
- WATERS V. L., GUINEY D. G., 1993. Processes at the nick region link conjugation, T-DNA transfer and rolling circle replication. Mol. Microbiol. 9, 1123-1130.
- WRÓBEL B., WEGRZYN G., 2002. Evolution of lambdoid replication modules. Virus Genes, 24, 163-171.
- ZHANG M., BROWN G. G., 1993. Structure of the maize mitochondrial RNAb and its relationship with other autonomously replicating RNA species. J. Mol. Biol. 230, 757-765.
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