References

Agapova SR, Andreeva AL, Starovoitov II, Vorob'eva LI, Terent'ev PB (1992) Plasmids for biodegradation of 2,6-dimethylpyridine, 2,4-dimethylpyridine, and pyridine in strains of Arthrobacter. Mol Gen Mikrobiol Virusol 1992 10-13 Aislabie J, Davison AD, Boul HL, Franzmann PD, Jardine DR, Karuso P (1999) Isolation of Terrabacter sp. strain DDE-1, which metabolizes when induced with biphenyl. Appl Environ Microbiol 65 5607-5611 Arai H, Kosono S, Taguchi K, Maeda M, Song E, Fuji F, Chung SY, Kudo T...

Linear Plasmids of Rhizoctonia solani

The plant pathogenic fungus R. solani has a wide range of hosts and is one of the most serious fungal pathogens in the world. Fungal isolates were assigned to incompatibility groups based on their affinities for hyphal fusion with members of designated anastomosis groups (AGs). Japanese isolates were divided into ten AGs (Anderson 1982 Ogoshi 1987 Carling et al. 2002). Of these, AG1, AG2-1, AG2-2, AG3, and AG4 correspond to sasakii type (IA) and web-blight type (IB), winter crop type (II), rush...

Circular Retroplasmid Replication

Studies of retroplasmid replication rely on analyzing polymerase activity in plasmid-containing ribonucleoprotein (RNP) particles isolated from mitochondria (Kuiper and Lambowitz 1988 Wang et al. 1992 Kennell et al. 1995 Walther and Kennell 1999) and characterization of in vivo replication intermediates (Stohl et al. 1982 Akins et al. 1986, 1989 Kennell et al. 1994 Nagasaka et al. 2003 Simpson et al. 2004). The limitations of efficiently transforming mitochondria outside of S. cerevisiae...

PSLA2L

SAP1 (no secondary metabolism genes) Fig. 7 Large linear plasmids vary greatly in their possession of gene sets for antibiotic biosynthesis. In the examples shown, SCP1 (365 kb) was initially studied for its fertility properties in S. coelicolor A3(2) pSLA2-L (211 kb), from S. rochei, was identified in a PFGE study of antibiotic-producing streptomycetes, and SAP1 (94 kb) was discovered in the course of genome sequencing of S. avermitilis (see Table 1 for references). The three plasmids shown...

Evolution of Linear Plasmids in Eukaryotes

Eukaryotic linear plasmids, either mitochondrial or cytoplasmic, in principle replicate like genomes of adenoviruses and phi29-like bacteriophages (see above), which has led to the conclusion that they share a common ancestor (Meinhardt et al. 1986, 1990 Kuzmin et al. 1988 Oeser and Tudzynski 1989 Rohe et al. 1992 Kempken et al. 1992). For reconstruction of the phylogeny, both DNA and RNA polymerases have been employed, since the respective genes were found in almost every linear plasmid...

Streptomyces coelicolor A32 Has a Plasmid Fertility Factor SCP1 Capable of Integration into the Chromosome to Give High

Sermonti and Casciano (1963) provided the first hints that different fertility types might be represented among strains derived from S. coelicolor A3(2). A subsequent large-scale systematic analysis was carried out (see Hopwood et al. 1973, for a review). Colonies from UV-exposed spores of one strain (number 12, and therefore an early derivative of the wild type) were replicated onto plates spread with untreated spores of mating partners with suitably different genetic markers, to allow growth,...

The pGKL1 Encoded Zymocin a Biogenesis

The K. lactis zymocin is a heterotrimeric (a, P, y) glycoprotein, the subunits of which display molecular masses of 99, 30, and 28 kDa, respectively (Stark and Boyd 1986). The smallest subunit (y) is encoded by ORF4 of pGKL1 the two larger ones originate from a single gene product (Orf2p) by posttrans-lational processing (Hishinuma et al. 1984 Stark et al. 1984, 1990 Sor and Fukuhara 1985 Stark and Boyd 1986 Tokunaga et al. 1987). Both Orf2p and Orf4p carry typical signal peptides mediating...

Dibenzofuran and Fluorene Oxidation via Angular Dioxygenation as well as the Protocatechuate Pathway are Encoded on

Catechol And Protocatechuate

Terrabacter sp. strain DBF63 is able to utilize both dibenzofuran and fluorene as sole source of carbon and energy (Monna et al. 1993) and to cometabo-lize a broad range of chlorinated dibenzo-p-dioxins and dibenzofurans (Habe et al. 2001, 2002). Dibenzofuran degradation is initiated by angular dioxy-genation, catalyzed by the oxygenase DbfA (with unknown electron transport proteins). The chemically unstable dihydrodiol formed in the enzymatic reaction is spontaneously rearomatized to...

Protelomerases are also Involved in Linear Plasmid Replication and Maintenance

The phage-encoded protelomerase is essential for the conversion of the phage genome into the linear plasmid prophage. Regions on the N15 and PY54 genomes that are important for plasmid maintenance have been defined by the construction of replicative linear and circular miniplasmid derivatives (Hertwig et al. 2003a Vostrov et al. 1992). It was demonstrated that for the replication of a circular miniplasmid, two phage-encoded loci are essential (1) the reading frame of the replication initiation...

Postreplicational Segregation

The Plasmid-Encoded parAB-parS System Low-copy-number linear plasmids of Streptomyces contain a pair of partitioning genes, parA and parB, which are involved in active segregation and thus stable inheritance of these plasmids. During segregation, ParB binds to a specific palindromic DNA sequence (parS) on the replicons and forms a partitioning complex, while ParA, an ATPase, forms cytoskeleton-like structures and is responsible for segregating the two daughter replicons (for review, see Gerdes...

The Telomere Resolvase ResT

Coincident with the work describing a telomere resolution step in vivo in B. burgdorferi, the telomere resolvase from the E. coli phage N15 was discovered (Deneke et al. 2000). It had been noted previously that the BBB03 locus of B. burgdorferi had an area of sequence homology with TelN, the protein later confirmed as the N15 telomere resolvase (Rybchin and Svarchevsky 1999). See Hertwig 2007 (this volume) for a review of telomere resolution in phage N15 and other related elements. The Borrelia...

Catabolic Gene Clusters of Rhodococcus sp RHA1 Are Distributed on Several Replicons

The genome of Rhodococcus sp. strain RHA1, a very potent biphenyl and PCB degrader, comprises a total of 9.7 Mb and consists of the 7.8-Mb chromosome and three linear plasmids pRHL1, pRHL2, and pRHL3 (McLeod et al. 2006 www.rhodococcus.ca). Genome analysis indicated that the three linear plasmids carry 11 of the 26 peripheral aromatic degradation pathways of strain RHA1, suggesting that they have a significant catabolic role and may serve as reservoirs for catabolic functions (McLeod et al....

Other Killer Plasmids and Encoded Toxins

Except for pGKL1, there are three nonautonomous linear plasmids from different yeast species known to encode killer toxins, i.e., pPac1-2 of P. acaciae, pPin1-3 of P. inositovora, and pWR1A of D. robertsiae (Gunge et al. 1981 Wor-sham and Bolen 1990 Hayman and Bolen 1991 Klassen and Meinhardt 2002). Each of the aforementioned elements encodes a chitin binding protein, structurally akin to the zymocin a-subunit (Klassen and Meinhardt 2002, 2003 Klassen et al. 2004). Additionally, hydrophobic...

Autonomous Elements

Extranuclear linear plasmids residing in the cytoplasm constitute the prevailing version of accessory genetic elements in yeast routinely, they exist Table 2 Yeast linear plasmids. Mitochondrial (pPH1, pPK1) and cytoplasmic linear plas-mids of ascomycetes and basidiomycetes (pTP1) are given along with their sizes (in kb) and coding capacity. DP DNA polymerase RP RNA polymerase T toxin I immunity CB chitin binding protein CE capping enzyme SSB single-strand binding protein TRF terminal...

Circular Retroplasmids

The Mauriceville plasmid of Neurospora crassa is a covalently closed circular DNA of approximately 3.6 kb. It has high sequence identity (97-99 ) with the Varkud, Maddur-1, and Maddur-2 plasmids of a related species, N. intermedia (Nargang et al. 1984 Akins et al. 1988 D'Souza et al. 2005). The 2.6 kb pThrl plasmid of Trichoderma harzianum is the only other circular retroplasmid reported outside of Neurospora species (Antal et al. 2002 Fig. 1). Recently, a possible related retroplasmid was...

Terminal DNA

The telomeric sequences of many linear chromosomes and plasmids of Streptomyces are available. The telomeric sequences of most Streptomyces linear plasmids characterized so far resemble those of Streptomyces chromosomes. The term archetypal is used here to describe this group of conserved telomeric sequences, which need to be distinguished from a number of atypical telomeres (such as SCP1, pRL1, pRL2, and the S. griseus chromosome see SAP1 SAP2 pSV2(r) pFRL1 PSCL1 pSLA2 S. lipmanii S. rimosus...

The Cytoplasmic Trancriptase Complex

A rather unique RNA polymerase, a DExH D box helicase and an mRNA capping enzyme, represent key elements of the cytoplasmic transcriptional apparatus. Consistent with their pivotal function, each of the above genes were proven essential for plasmid maintenance (Schaffrath et al. 1995, 1997 Larsen et al. 1998). The RNA polymerase (Fig. 3) appears to consist of two different subunits, encoded by pGKL2 ORF6 and ORF7, and homologous genes in other plasmid systems. The architecture of the enzyme...

Interactions of Linear Plasmids with the Chromosome Physical Analysis

The physical isolation of SCP1 (Kinashi and Shimaji-Murayama 1991) was followed by the cloning of segments of SCP1 in cosmids and the establishment of a restriction map (Redenbach et al. 1998), and eventually the sequencing of the plasmid (Bentley et al. 2004) and the chromosome of its host (Bentley et al. 2002). It became possible to investigate the physical basis of some of the chromosome-donating strains described above. Integration of SCP1 Within the Chromosome The first SCP1-chromosome...

Introduction

Mitochondrial (mt) plasmids are defined as small (< 1-15 kb), autonomously replicating genetic elements that show no significant homology to mitochondrial DNA and have independent evolutionary origins. They are structurally diverse and are widely distributed in certain taxa (e.g., filamentous fungi), yet absent in others (e.g., animals see Chap. 9, in this volume). They differ from bacterial plasmids in several important areas most mt plasmids encode their own polymerase(s) that control key...

Linear Plasmids and Evolution

It is likely that the linearity of Streptomyces chromosomes originally resulted from Campbell-type recombination between a circular genome and a linear plasmid Volff and Altenbuchner 2000 Chen et al. 2002 . Although it has been suggested that this occurred many times independently within the Streptomyces lineage Chen et al. 2002 , it is also attractive to consider the case for a unitary linearisation event at the birth of the genus. On the assumption that diverse linear plasmids continued to...

Modular Organization and Different Genomic Localization of Naphthalene Degradation Genes in Strains I24 P200 P400

I24 is able to utilize naphthalene and toluene as carbon sources, and to co-oxidize indene. The naphthalene inducible genes nidABCD Fig. 7 coding for naphthalene dioxygenase, a dehydrogenase, and a putative aldolase Treadway et al. 1999 reside on an 80-kb plasmid AF45237.2 Priefert et al. 2004 Table 1 . Common initial steps in naphthalene degradation by Rhodococcus sp. strains NCIMB12038, P200, and P400 likewise involve formation of the cis-naphthalene dihydrodiol, catalyzed by...

Terminal Proteins

The first Streptomyces TPs characterized were found to be highly conserved in size 184-185 amino acids aa and sequence Fig. 2a Bao and Cohen 2001 Yang et al. 2002 . No similarity to other known protein sequences in the databases including the TPs of adenoviruses and 29 was found. They are herein designated archetypal TPs to distinguish them from the heterologous TP that caps SCP1 see below . Bao and Cohen designated the gene encoding archetypal TPs as tpg followed by a letter and sometimes a...

And Linear Plasmids are Widespread Among Streptomycetes

Since SCPl behaved in many ways similarly to well-characterised plasmids such as the F-factor of E. coli, it was reasonable to suppose that it would be physically similar as well. It was therefore natural to try to isolate it by CsCl-ethidium bromide density gradient centrifugation. Application of this technique to S. coelicolor indeed yielded CCC DNA, of about 30 kb Schrempf et al. l975 , but this proved to be present even in SCPl-free strains, and was designated SCP2 Bibb et al. l977 ....

Virulence Determinants on the Linear Plasmid pFiD188

Two of the four loci of region U1, fas and att, are fundamental for virulence and have been extensively studied Goethals et al. 2001 . The fas locus codes for the most important pathogenicity factor of R. fascians and mutations lead to a nonvirulent phenotype. The locus contains an operon of six open reading frames ORFs that encode the machinery for the synthesis of a cytokinin-like signal molecule essential for symptom development Crespi et al. 1994 Fig. 3 . The gene product of orf 1 is...

On Linear Plasmids in Phylogenetically Different Bacteria

Since chloroethenes, which include known or suspected carcinogens, are widely distributed at many contaminated sites, their microbial degradation has been investigated intensely, and aerobic as well as anaerobic transformation pathways have been described for a review, see Fetzner 1998a . Linear plasmids have been implicated in alkene and chloroethene metabolism by phylogenetically very different bacteria, such as Mycobacterium strains, Gor-donia rubripertincta B-276 formerly Rhodococcus...

Alkane Oxidation Genes Located on pREL1 of Rhodococcus erythropolis PR4

Rhodococcus erythropolis PR4, an alkane degrading strain, contains the linear plasmid pREL1 and two circular plasmids pREC1 and pREC2 Table 1 , which have been sequenced completely Sekine et al. 2006 . The plasmids contain modular segments that are homologous to corresponding regions of other rhodococcal plasmids. While pREL1 shares several regions of homology with pBD2 of R. erythropolis strain BD2, putative alkane degradation genes, organized in two clusters and flanked by transposon and...