The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism

Garcillán-Barcia, M. Pilar; Pluta, Radoslaw; Lorenzo-Díaz, Fabián; Bravo, Alicia; Espinosa, Manuel

doi:10.1128/mmbr.00222-20

Cited by 16 publications

(20 citation statements)

References 312 publications

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“…All 63 members of the RepL type were single-replicon small plasmids with sizes ranging from 2.4 to 2.7 kb, and their high prevalence among S. aureus had been previously reported [ 38 , 44 , 52 ]. These plasmids, which belonged to the pSN2 family [ 53 ], encode the replicase gene, a hypothetical protein-coding sequence, and an ermC gene, which confers resistance to macrolides, lincosamides, and streptogramin B (MLS B ) antibiotics ( Supplementary Figure S1 ). The sequence variations observed in these plasmids were either in the non-coding sequences or the ermC upstream regulatory sequence, which will be discussed in a later section on antimicrobial resistance.…”

Section: Resultsmentioning

confidence: 99%

The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia

et al. 2023

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Methicillin-resistant Staphylococcus aureus (MRSA) is a priority nosocomial pathogen with plasmids playing a crucial role in its genetic adaptability, particularly in the acquisition and spread of antimicrobial resistance. In this study, the genome sequences of 79 MSRA clinical isolates from Terengganu, Malaysia, (obtained between 2016 and 2020) along with an additional 15 Malaysian MRSA genomes from GenBank were analyzed for their plasmid content. The majority (90%, 85/94) of the Malaysian MRSA isolates harbored 1–4 plasmids each. In total, 189 plasmid sequences were identified ranging in size from 2.3 kb to ca. 58 kb, spanning all seven distinctive plasmid replication initiator (replicase) types. Resistance genes (either to antimicrobials, heavy metals, and/or biocides) were found in 74% (140/189) of these plasmids. Small plasmids (<5 kb) were predominant (63.5%, 120/189) with a RepL replicase plasmid harboring the ermC gene that confers resistance to macrolides, lincosamides, and streptogramin B (MLSB) identified in 63 MRSA isolates. A low carriage of conjugative plasmids was observed (n = 2), but the majority (64.5%, 122/189) of the non-conjugative plasmids have mobilizable potential. The results obtained enabled us to gain a rare view of the plasmidomic landscape of Malaysian MRSA isolates and reinforces their importance in the evolution of this pathogen.

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Section: Resultsmentioning

confidence: 99%

The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia

et al. 2023

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“…Notably, some rolling-circle replication proteins (RC-Rep) act as replicative relaxases ( 37 ). They interact with the MPF system of a conjugative element and trigger plasmid conjugation in an oriT -independent manner ( 53 ). We searched for these proteins to test if this alternative pathway could be involved in the mobilization of plasmids lacking oriT and classical relaxases.…”

Section: Resultsmentioning

confidence: 99%

Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation

Ares-Arroyo

Coluzzi

Rocha

2022

Nucleic Acids Research

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Plasmids can be transferred between cells by conjugation, thereby driving bacterial evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer for many plasmids because they lack all protein-coding genes required for conjugation. We solved this conundrum by identifying hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus. These plasmids (pOriT) hijack the relaxases of conjugative or mobilizable elements, but not both. The functional dependencies between pOriT and other plasmids explain their co-occurrence: pOriT are abundant in cells with many plasmids, whereas conjugative plasmids are the most common in the others. We systematically characterized plasmid mobility in relation to conjugation and alternative mechanisms of transfer and can now propose a putative mechanism of transfer for ∼90% of them. In most cases, plasmid mobility seems to involve conjugation. Interestingly, the mechanisms of mobility are important determinants of plasmid-encoded accessory traits, since pOriTs have the highest densities of antimicrobial resistance genes, whereas plasmids lacking putative mechanisms of transfer have the lowest. We illuminate the evolutionary relationships between plasmids and suggest that many pOriT may have arisen by gene deletions in other types of plasmids. These results suggest that most plasmids can be transferred by conjugation.

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“…We also deem it unlikely that the intermediate reflects rolling-circle replication of ERCs. Although rolling-circle replication features long single-stranded tails (Garcillan-Barcia et al, 2022), the presence of the intermediate does not correlate with ERC levels: fob1 mutants, which have strongly reduced ERC levels (Defossez et al, 1999), form wild-type levels of the intermediate, whereas top1 mutants have increased ERC levels but no intermediate.…”

Section: Discussionmentioning

confidence: 99%

Topoisomerase I promotes formation of a novel DNA intermediate in the ribosomal DNA

Molinar

Sultanov

Klein

et al. 2022

Preprint

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The ribosomal DNA (rDNA) is a conserved but highly unstable multi-gene locus that codes for the RNA components of the ribosome (rRNA). Despite being essential for protein translation and survival, rRNA gene-copy numbers fluctuate frequently. Here, we describe a novel rDNA intermediate that may be involved in these copy-number changes in Saccharomyces cerevisiae. Two-dimensional gel analyses revealed a structure that includes a large single-stranded tail and arises from the promoter of the 35S rRNA gene. Formation of this intermediate is unaffected by reduced 35S transcription but relies on topoisomerase I (Top1). Unexpectedly, intermediate formation is also independent of S phase or the rDNA-instability factor Fob1, even though Fob1 is mediates the major peak of Top1 cleavage complexes in the rDNA. Indeed, we find that the known rDNA instability phenotypes of top1 mutants, including increased formation of extrachromosomal rDNA circles, elevated genetic marker loss, and instability of critically short rDNA arrays, are also largely independent of Fob1. We therefore speculate that failure to form this intermediate leads to rDNA instability in top1 mutants.

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The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism

Abstract: Plasmids are self-replicative DNA elements that are transferred between bacteria. Plasmids encode not only antibiotic resistance genes but also adaptive genes that allow their hosts to colonize new niches.

Cited by 16 publications

References 312 publications

The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia

The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia

Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation

Topoisomerase I promotes formation of a novel DNA intermediate in the ribosomal DNA

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