Liniowe plazmidy bakteryjne

• Authors: Małgorzata Łobocka

Title variants

EN

Linear bacterial plasmids

• Languages of publication: PL EN

Abstracts

EN

Summary Completion of linear DNA replication requires a way to restore the original sequence and structure of linear DNA ends which can not be fully replicated by conventional DNA polymerases. In bacteria, the end replication problem has been circumvented through the use of circular plasmids and chromosomes. However linear bacterial plasmids and chromosomes have also been isolated. Their ends, commonly known as prokaryotic telomers, differ in structure from the ends of eukaryotic chromosomes and, during replication, become restored to their original form by a different mechanism. Two kinds of linear plasmids have been isolated: plasmids with covalently closed hairpin ends, and plasmids with invertron ends, which contain proteins bound to their 5' termini. The latter constitute the larger group and are commonly found in actinomycetous bacteria. They are usually conjugative and confer advantageous phenotypes. Plasmids with covalently closed ends are common in spirochetes of the genus Borrelia. A model plasmid of this group is prophage N15 of Escherichia coli, which exists in lysogens as a linear DNA molecule. The major difference between circular and linear plasmids is the presence in the latter of linear ends and proteins that specifically recognize those ends and are able to restore plasmid linearity during or after replication. Complete replication of invertron telomers depends on their 5' end-associated proteins but its mechanism is still unclear. Plasmids with covalently closed ends are completely replicated from an internal origin to form circular dimeric molecules that can be observed as replication intermediates. Further processing of the intermediates depends on telomere resolution, a DNA breakage and reunion reaction, in which opposite strands of replicated telomeres are cleaved and rejoined to form covalently closed ends of two progeny molecules.

• Journal: Kosmos
• Year: 2002
• Volume: 51
• Issue: 3
• Pages: 283-296

Dates

published

2002

Contributors

author

Małgorzata Łobocka

• Zakład Biochemii Drobnoustrojów Instytut Biochemii i Biofizyki PAN, Pawińskiego 5A, 02-106 Warszawa, Polska

References

• BAO K., COHEN S. N., 2001. Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces. Genes Dev. 15, 1518-1527.
• BERGERON H., LABBE D., TURMEL C., LAU P. C., 1998. Cloning, sequence and expression of a linear plasmid-based and a chromosomal homolog of chloroacetaldehyde dehydrogenase-encoding genes in Xanthobacter autotrophicus GJ10. Gene 207, 9-18.
• BEY S. J., TSOU M. F., HUANG C. H., YANG C. C., CHEN C. W., 2000. The homologous terminal sequence of the Streptomyces lividans chromosome and SLP2 plasmid. Microbiology 146, 911-922.
• BHATT A., KIESER H. M., MELTON R. E., KIESER T., 2002. Plasmid transfer from Streptomyces to Mycobacterium smegmatis by spontaneous transformation. Mol. Microbiol. 43, 135-146.
• BROWN S. E., KNUDSON D. L., ISHIMARU C. A., 2002. Linear plasmid in the genome of Clavibacter michiganensis subsp. sepedonicus. J. Bacteriol. 184, 2841-2844.
• CALCUTT M. J., SCHMIDT F. J., 1992. Conserved gene arrangement in the origin region of the Streptomyces coelicolor chromosome. J. Bacteriol. 174, 3220-3226.
• CASJENS S., 1999. Evolution of the linear DNA replicons of the Borrelia spirochetes. Curr. Opin. Microbiol. 2, 529-534.
• CASJENS S., MURPHY M., DE LANGE M., SAMPSON L., VAN VUGT R., HUANG W. M., 1997. Telomeres of the linear chromosomes of Lyme disease spirochaetes: nucleotide sequence and possible exchange with linear plasmid telomeres. Mol. Microbiol. 26, 581-596.
• CASJENS S., PALMER N., VAN VUGT R., HUANG W. M., STEVENSON B., ROSA P., LATHIGRA R., SUTTON G., PETERSON J., DODSON R. J., HAFT D., HICKEY E., GWINN M., WHITE O., FRASER C. M., 2000. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol. Microbiol. 35, 490-516.
• CHACONAS G., STEWART P. E., TILLY K., BONO J. L., ROSA P., 2001. Telomere resolution in the Lyme disease spirochete. EMBO J. 20, 3229-3237.
• CHANG P. C., COHEN S. N., 1994. Bidirectional replication from an internal origin in a linear Streptomyces plasmid. Science 265, 952-954.
• CHANG P. C., KIM E. S., COHEN S. N., 1996. Streptomyces linear plasmids that contain a phage-like, centrally located, replication origin. Mol. Microbiol. 22, 789-800.
• CHEN C. W., YU T. W., LIN Y. S., KIESER H. M., HOPWOOD D. A., 1993. The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule. Mol. Microbiol. 7, 925-932.
• DABROCK B., KESSELER M., AVERHOFF B. i GOTTSCHALK G. 1994. Identification i characterization of a transmissible linear plasmid from Rhodococcus erythropolis BD2 that encodes isopropylbenzene and trichloroethene catabolism. Appl. Environ. Microbiol. 60, 853-860.
• DENEKE J., ZIEGELIN G., LURZ R., LANKA E., 2000. The protelomerase of temperate Escherichia coli phage N15 has cleaving- joining activity. Proc. Natl. Acad. Sci. USA 97, 7721-7726.
• DENEKE J., ZIEGELIN G., LURZ R., LANKA E., 2002. Phage N15 telomere resolution. Target requirements for recognition and processing by the protelomerase. J. Biol. Chem. 277, 10410-10419.
• FERDOWS M. S., SERWER P., GRIESS G. A., NORRIS S. J., BARBOUR A. G., 1996. Conversion of a linear to a circular plasmid in the relapsing fever agent Borrelia hermsii. J. Bacteriol. 178, 793-800.
• FISCHER G., HOLL A. C., VOLFF J. N., VIEWIELE D., DECARIS B., LEBLOND P., 1998. Replication of the linear chromosomal DNA from the centrally located oriC of Streptomyces ambofaciens revealed by PFGE gene dosage analysis. Res. Microbiol. 149, 203-210.
• FUKUDA M., SHIMIZU S., OKITA N., SETO M., MASAI E., 1998. Structural alteration of linear plasmids encoding the genes for polychlorinated biphenyl degradation in Rhodococcus strain RHA1. Antonie Van Leeuwenhoek, 74, 169-173.
• GOETHALS K., VEREECKE D., JAZIRI M., VAN MONTAGU M. i HOLSTERS M., 2001. Leafy gall formation by Rhodococcus fascians. Annu. Rev. Phytopathol. 39, 27-52.
• GOODNER B., HINKLE G., GATTUNG S., MILLER N., BLANCHARD M., QUROLLO B., GOLDMAN B. S., CAO Y., ASKENAZI M., HALLING C., MULLIN L., HOUMIEL K., GORDON J., VAUDIN M., IARTCHOUK O., EPP A., LIU F., WOLLAM C., ALLINGER M., DOUGHTY D., SCOTT C., LAPPAS C., MARKELZ B., FLANAGAN C., CROWELL C., GURSON J., LOMO C., SEAR C., STRUB G., CIELO C., SLATER S., 2001. Genome sequence of the plant pathogen i biotechnology agent Agrobacterium tumefaciens C58. Science 294, 2323-2328.
• GOSHI K., UCHIDA T., LEZHAVA A., YAMASAKI M., HIRATSU K., SHINKAWA H., KINASHI H., 2002. Cloning and analysis of the telomere i terminal inverted repeat of the linear chromosome of Streptomyces griseus. J. Bacteriol. 184, 3411-3415.
• GRAVIUS B., GLOCKER D., PIGAC J., PIZA K., HRANUELI D., CULLUM J., 1994. The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its interactions with the chromosome. Microbiology 140, 2271-2277.
• GRIGORIEV P., ŁOBOCKA M. B., 2001. Determinants of segregational stability of the linear plasmid prophage N15 of Escherichia coli. Mol. Microbiology 42, 355-368.
• HINNEBUSCH J., BARBOUR A. G., 1991. Linear plasmids of Borrelia burgdorferi have a telomeric structure and sequence similar to those of a eukaryotic virus. J. Bacteriol. 173, 7233-7239.
• HINNEBUSCH J., TILLY K., 1993. Linear plasmids and chromosomes in bacteria. Mol. Microbiol. 10, 917-922.
• HIRATSU K., MOCHIZUKI S., KINASHI H., 2000. Cloning i analysis of the replication origin and the telomeres of the large linear plasmid pSLA2-L in Streptomyces rochei. Mol. Gen. Genet. 263, 1015-1021.
• HUANG C. H., LIN Y. S., YANG Y. L., HUANG S. W., CHEN C. W., 1998. The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures. Mol. Microbiol. 28, 905-916.
• KALKUS J., DORRIE C., FISCHER D., REH M., SCHLEGEL H. G., 1993. The giant linear plasmid pHG207 from Rhodococcus sp. encoding hydrogen autotrophy: characterization of the plasmid and its termini. J. Gen. Microbiol. 139, 2055-2065.
• KALKUS J., MENNE R., REH M., SCHLEGEL H. G., 1998. The terminal structures of linear plasmids from Rhodococcus opacus. Microbiology 144, 1271-1279.
• KESSELER M., DABBS E. R., AVERHOFF B., GOTTSCHALK G., 1996. Studies on the isopropylbenzene 2, 3- dioxygenase and the 3- isopropylcatechol 2,3-dioxygenase genes encoded by the linear plasmid of Rhodococcus erythropolis BD2. Microbiology 142, 3241-3251.
• KIESERK H. M., KIESERK T., HOPWOOD D. A., 1992. A combined genetic and physical map of the Streptomyces coelicolor A3(2) chromosome. J. Bacteriol. 174, 5496-5507.
• KING A. J., VAN DER VLIET P. C., 1994. A precursor terminal protein-trinucleotide intermediate during initiation of adenovirus DNA replication: regeneration of molecular ends in vitro by a jumping back mechanism. EMBO J. 13, 5786-5792.
• KOBRYN K., CHACONAS G., 2001. The circle is broken: telomere resolution in linear replicons. Curr. Opin. Microbiol. 4, 558-564.
• KOBRYN K., CHACONAS G., 2002. ResT, a telomere resolvase encoded by the Lyme disease spirochete. Mol. Cell 9, 195-201.
• KRUM J. G., ENSIGN S. A., 2001. Evidence that a linear megaplasmid encodes enzymes of aliphatic alkene and epoxide metabolism i coenzyme M 2-mercaptoethanesulfonate) biosynthesis in Xanthobacter strain Py2. J. Bacteriol. 183, 2172-2177.
• LE DANTEC C., WINTER N., GICQUEL B., VINCENT V., P ICARDEAU M., 2001. Genomic sequence and transcriptional analysis of a 23-kilobase mycobacterial linear plasmid: evidence for horizontal transfer and identification of plasmid maintenance systems. J. Bacteriol. 183, 2157-2164.
• MASAI E., SUGIYAMA K., IWASHITA N., SHIMIZU S., HAUSCHILD J. E., HATTA T., KIMBARA K., YANO K., FUKUDA M., 1997. The bphDEF meta-cleavage pathway genes involved in biphenyl/polychlorinated biphenyl degradation are located on a linear plasmid and separated from the initial bphACB genes in Rhodococcus sp. strain RHA1. Gene 187, 141-149.
• MEIJER W. J., HORCAJADAS J. A., SALAS M., 2001. Phi29 family of phages. Microbiol. Mol. Biol. Rev. 65, 261-287.
• MEINHARDT F., SCHAFFRATH R., LARSEN M., 1997. Microbial linear plasmids. Appl. Microbiol. Biotechnol. 47, 329-336.
• MUSIALOWSKI M. S., FLETT F., SCOTT G. B., HOBBS G., SMITH C. P., OLIVER S. G., 1994. Functional evidence that the principal DNA replication origin of the Streptomyces coelicolor chromosome is close to the dnaA-gyrB region. J. Bacteriol. 176, 5123-5125.
• NETOLITZKY D. J., WU X., JENSEN S. E., ROY K. L., 1995. Giant linear plasmids of beta-lactam antibiotic producing Streptomyces. FEMS Microbiol. Lett. 131, 27-34.
• PALMER N., FRASER C., CASJENS S., 2000. Distribution of twelve linear extrachromosomal DNAs in natural isolates of Lyme disease spirochetes. J. Bacteriol. 182, 2476-2480.
• PIZA K., PFALZER G., CULLUM J., HRANUELI D., 1997. Physical mapping shows that the unstable oxytetracycline gene cluster of Streptomyces rimosus lies close to one end of the linear chromosome. Microbiology 143, 1493-1501.
• PIZA S., BIUKOVIC G., PARAVIC A., DADBIN A., CULLUM J., HRANUELI D., 1998. Recombination between the linear plasmid pPZG101 and the linear chromosome of Streptomyces rimosus can lead to exCHANGe of ends. Mol. Microbiol. 28, 1165-1176.
• PANG X., SUN Y., LIU J., ZHOU X., DENG Z., 2002. A linear plasmid temperature-sensitive for replication in Streptomyces hygroscopicus 10-22. FEMS Microbiol. Lett. 208, 25-28.
• PICARDEAU M., LE DANTEC C., VINCENT V., 2000. Analysis of the internal replication region of a mycobacterial linear plasmid. Microbiology 146, 305-313.
• PICARDEAU M., VINCENT V., 1997. Characterization of large linear plasmids in mycobacteria. J. Bacteriol. 179, 2753-2756.
• PICARDEAU M., VINCENT V., 1998. Mycobacterial linear plasmids have an invertron-like structure related to other linear replicons in actinomycetes. Microbiology 144, 1981-1988.
• QIN Z., COHEN S. N., 1998. Replication at the telomeres of the Streptomyces linear plasmid pSLA2. Mol. Microbiol. 28, 893-903.
• RAVEL J., DIRUGGIERO J., ROBB F. T., HILL R. T., 2000. Cloning and sequence analysis of the mercury resistance operon of Streptomyces sp. Strain CHR28 reveals a novel putative second regulatory gene. J. Bacteriol. 182, 2345-2349.
• RAVEL J., SCHREMPF H., HILL R. T., 1998. Mercury resistance is encoded by transferable giant linear plasmids in two chesapeake bay Streptomyces strains. Appl. Environ. Microbiol. 64, 3383-3388.
• RAVIN N. V., STRAKHOVA T. S., KUPRIANOV V. V., 2001. The protelomerase of the phage-plasmid N15 is responsible for its maintenance in linear form. J. Mol. Biol. 312, 899-906.
• RAVIN V., RAVIN N., CASJENS S., FORD M. E., HATFULL G. F., HENDRIX R. W., 2000. Genomic sequence and analysis of the atypical temperate bacteriophage N15. J. Mol. Biol. 299, 53-73.
• REDENBACH M., BIBB M., GUST B., SEITZ B., SPYCHAJ A., 1999. The linear plasmid SCP1 of Streptomyces coelicolor A3(2) possesses a centrally located replication origin and shows significant homology to the transposon Tn4811. Plasmid 42, 174-185.
• ROUSSEL Y., COLMIN C., SIMONET J. M., DECARIS B., 1993. Strain characterization, genome size andplasmid content in the Lactobacillus acidophilus group (Hansen i Mocquot). J. Appl. Bacteriol. 74, 549-556.
• RYBCHIN V. N., SVARCHEVSKY A. N., 1999. The plasmid prophage N15: a linear DNA with covalently closed ends. Mol. Microbiol. 33, 895-903.
• SVEKI H., AKIRA M., FURUHASHI K., AVERHOFF B., GOTTSCHALK G., 1999. Degradation of trichloroethene by a linear-plasmid-encoded alkene monooxygenase in Rhodococcus corallinus (Nocardia corallina) B-276. Microbiology 145, 1721-1730.
• SAKAGUCHI K., 1990. Invertrons, a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and genomes of adeno-type viruses. Microbiol. Rev. 54, 66-74.
• SALAS M., 1999. Mechanisms of initiation of linear DNA replication in prokaryotes. Genet. Eng. 21, 159-171.
• SHIFFMAN D., COHEN S. N., 1992. Reconstruction of a Streptomyces linear replicon from separately cloned DNA fragments: existence of a cryptic origin of circular replication within the linear plasmid. Proc. Natl. Acad. Sci. USA 89, 6129-6133.
• SHIMIZU S., KOBAYASHI H., MASAI E., FUKUDA M., 2001. Characterization of the 450-kb linear plasmid in a polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 67, 2021-2028.
• SPATZ K., KOHN H., REDENBACH M., 2002. Characterization of the Streptomyces violaceoruber SANK95570 plasmids pSV1 and pSV2. FEMS Microbiol. Lett. 213, 87-92.
• STOLL A., HORVAT L. I., LOPES-SHIKIDA S. A., PADILLA G., CULLUM J., 2000. Isolation and cloning of Streptomyces terminal fragments. Antonie Van Leeuwenhoek, 78, 223-236.
• TAKAHASHI Y., CUTLER S. J., FUKUNAGA M., 2000. Size conversion of a linear plasmid in the relapsing fever agent Borrelia duttonii. Microbiol. Immunol. 44, 1071-1074.
• UZ I., DUAN Y. P., OGRAM A., 2000. Characterization of the naphthalene-degrading bacterium, Rhodococcus opacus M213. FEMS Microbiol. Lett. 185, 231-238.
• VOLFF J. N., ALTENBUCHNER J., 2000. A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol. Lett. 186, 143-150.
• WIENER P., EGAN S., HUDDLESTON A. S., WELLINGTON E. M., 1998. Evidence for transfer of antibiotic-resistance genes in soil populations of streptomycetes. Mol. Ecol. 7, 1205-1216.
• WILLEMS H., JAGER C., BALJER G., 1998. Physical and genetic map of the obligate intracellular bacterium Coxiella burnetii. J. Bacteriol. 180, 3816-3822.
• YANG C. C., HUANG C. H., LI C. Y., TSAY Y. G., LEE S. C., CHEN C. W., 2002. The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins. Mol. Microbiol. 43, 297-305.
• YANG M. C., LOSCICK R., 2001. Cytological evidence for association of the ends of the linear chromosome in Streptomyces coelicolor. J. Bacteriol. 183, 5180-5186.
• ZAKRZEWSKA-CZERWINSKA J., SCHREMPF H., 1992. Characterization of an autonomously replicating region from the Streptomyces lividans chromosome. J. Bacteriol. 174, 2688-2693.