The patchwork nature of rolling-circle plasmids: comparison of six plasmids from two distinct Bacillus thuringiensis serotypes

Andrup, Lars; Jensen, Gert B.; Wilcks, Andrea; Smidt, Lasse; Hoflack, Lieve; Mahillon, Jacques

doi:10.1016/s0147-619x(03)00015-5

Cited by 49 publications

(57 citation statements)

References 109 publications

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“…Bacilli harbor a large variety of plasmids, which include a linear species of Ϸ15 kb (2,13,15,31,34). Recently, the genome sequencing of Bacillus cereus ATCC 14579 revealed the sequence of a linear plasmid (pBClin15) of 15,100 bp (19).…”

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The Bacillus thuringiensis Linear Double-Stranded DNA Phage Bam35, Which Is Highly Similar to the Bacillus cereus Linear Plasmid pBClin15, Has a Prophage State

et al. 2003

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Bam35, a 15-kbp double-stranded DNA phage, infects Bacillus thuringiensis. Recently, sequencing of the related Bacillus cereus revealed a 15.1-kbp linear plasmid, pBClin15. We show that pBClin15 closely resembles Bam35 and demonstrate conversion of Bam35 to a prophage. This state is common, as several B. thuringiensis strains release Bam35-related viruses.Phage Bam35 was originally isolated from Bacillus thuringiensis var. alesti strain 35 (1). As Bam35 could also be isolated from Bam35-resistant colonies of Bacillus megaterium and from a sensitive strain of B. thuringiensis var. entomocidus, a carrier state has been proposed (1). Recently, a clear-plaque mutant (Bam35c) was sequenced and further characterized (25). This work showed that Bam35 is related to PRD1, a linear double-stranded DNA virus with 5Ј-terminal proteins and an internal lipid membrane (4). PRD1 infects gram-negative bacteria harboring an IncP, -W, or -N conjugative plasmid. Structural analyses of PRD1 have, surprisingly, indicated that this member of the Tectiviridae is similar to the Adenoviridae, Phycodnaviridae, and Iridoviridae, which all infect eukaryotic hosts (9,24,33). This has led to the hypothesis that all these viruses belong to the same lineage, with a common ancestor existing before the separation of the three domains of life (5, 6).Phage Bam35 is closely related to Bacillus cereus plasmid pBClin15. Bacilli harbor a large variety of plasmids, which include a linear species of Ϸ15 kb (2,13,15,31,34). Recently, the genome sequencing of Bacillus cereus ATCC 14579 revealed the sequence of a linear plasmid (pBClin15) of 15,100 bp (19). While studying Bam35, we matched putative genes of the pBClin15 plasmid in independent database searches for the Bam35c coat protein and ATPase. After submission of this note, the nucleotide sequence of a linear B. thuringiensis plasmid, pGIL01, which differs from the Bam35c sequence by only approximately 10 nucleotides was published (32).To investigate the relationship of pBClin15 to Bam35c (14,935 bp), their genomes were compared. The organizations of the open reading frames (ORFs) of pBClin15 and those of Bam35c are highly similar (Fig. 1). Moreover, their sequences agree with 45 to 81% identity. The corresponding amino acids have 18 to 88% identity ( Table 1). The gene identification of Bam35c (25) was based on the reasonably detailed understanding of the corresponding PRD1 genes (7,8,16). A similar annotation shows that pBClin15 is related to Bam35 and PRD1 (Table 1). Among the most conserved genes in pBClin15 are those assigned to viral capsid components. These include the major coat protein 15 (corresponding to PRD1 protein P3) and the unique vertex packaging proteins 12, 14, and 16 (proteins P9, P20, and P22, respectively, in PRD1). Interestingly, the most conserved protein corresponds to a LexA-type transcription regulator (17, 21) homologue found in Bam35 but absent in PRD1.We then explored the relationship between pBClin15, Bam35c, and PRD1 by comparing their major coat proteins. First, the th...

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The Bacillus thuringiensis Linear Double-Stranded DNA Phage Bam35, Which Is Highly Similar to the Bacillus cereus Linear Plasmid pBClin15, Has a Prophage State

et al. 2003

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“…The presence of shsp-containing plasmids has been reported to increase cell survival at the high temperatures reached during different stages of fermentation in the dairy industry (27). Another striking example is the presence, in some Bacillus thuringiensis plasmids, of open reading frames encoding collagen-like proteins that are thought to play a role in aggregation formation or in adherence to other cells or substrates (28). RCR plasmids are considered to contain promiscuous replicons, as many of them have been shown to replicate in species, genera, or even phyla other than those from which they were isolated (25).…”

Section: General Aspects Of Plasmid Rolling-circle Replicationmentioning

confidence: 99%

Plasmid Rolling-Circle Replication

et al. 2015

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Plasmids are DNA entities that undergo controlled replication independent of the chromosomal DNA, a crucial step that guarantees the prevalence of the plasmid in its host. DNA replication has to cope with the incapacity of the DNA polymerases to start de novo DNA synthesis, and different replication mechanisms offer diverse solutions to this problem. Rolling-circle replication (RCR) is a mechanism adopted by certain plasmids, among other genetic elements, that represents one of the simplest initiation strategies, that is, the nicking by a replication initiator protein on one parental strand to generate the primer for leading-strand initiation and a single priming site for lagging-strand synthesis. All RCR plasmid genomes consist of a number of basic elements: leading strand initiation and control, lagging strand origin, phenotypic determinants, and mobilization, generally in that order of frequency. RCR has been mainly characterized in Gram-positive bacterial plasmids, although it has also been described in Gram-negative bacterial or archaeal plasmids. Here we aim to provide an overview of the RCR plasmids' lifestyle, with emphasis on their characteristic traits, promiscuity, stability, utility as vectors, etc. While RCR is one of the best-characterized plasmid replication mechanisms, there are still many questions left unanswered, which will be pointed out along the way in this review.

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“…(1) Plasmids that use a theta replication mechanism, which are normally large plasmids, such as p43, p44, p60, pAW63 and pBtoxis (Baum and Gilbert 1991;Wilcks et al 1999;Tang et al 2006); however, there are small plasmids such as pHT1030 that replicates by the theta mechanism (Lereclus and Arantes 1992). (2) Plasmids that usually replicate by a rolling-circle mechanism, which are mainly small plasmids, such as pTX14-1, pTX14-2, pTX14-3, pGI1, pGI2, pGI3, pUIBI1 and pBMBt1 (Andrup et al 2003;López-Meza et al 2003;Loeza-Lara et al 2005).…”

Section: Plasmids In Bacillus Thuringiensismentioning

confidence: 99%

Shuttle Vectors of Bacillus thuringiensis

Ochoa‐Zarzosa

López‐Meza

2012

Bacillus Thuringiensis Biotechnology

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Bacillus thuringiensis is characterized by the synthesis of parasporal crystals during sporulation; these are composed of one or more highly specific insecticidal or nematocidal endotoxin proteins. Genetic manipulation of B. thuringiensis has been achieved due to the development of stable shuttle vectors and the establishment of efficient transformation systems. Shuttle vectors of B. thuringiensis have been constructed using essentially replicons from resident plasmids from this bacterium that replicate by the theta mechanism. Also, these vectors have been developed using plasmid replicons from other Gram-positive bacteria or RCR plasmids. The transformation of B. thuringiensis with these vectors has been accomplished mainly through electroporation. The development of shuttle vectors with better characteristics and protocols with high transformation efficiency have greatly facilitated basic research and engineering of B. thuringiensis.

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The patchwork nature of rolling-circle plasmids: comparison of six plasmids from two distinct Bacillus thuringiensis serotypes

Cited by 49 publications

References 109 publications

The Bacillus thuringiensis Linear Double-Stranded DNA Phage Bam35, Which Is Highly Similar to the Bacillus cereus Linear Plasmid pBClin15, Has a Prophage State

The Bacillus thuringiensis Linear Double-Stranded DNA Phage Bam35, Which Is Highly Similar to the Bacillus cereus Linear Plasmid pBClin15, Has a Prophage State

Plasmid Rolling-Circle Replication

Shuttle Vectors of Bacillus thuringiensis

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