scholarly journals Effect of the CopB Auxiliary Replication Control System on Stability of Maintenance of Par+ Plasmid R1

2004 ◽  
Vol 186 (1) ◽  
pp. 207-211 ◽  
Author(s):  
Jan A. Olsson ◽  
Johan Paulsson ◽  
Kurt Nordström
Keyword(s):  
Copy Number ◽  
High Concentration ◽  
Average Cell ◽  
Initiator Protein ◽  
Plasmid R1 ◽  
Copy Numbers ◽  
Low Copy Number ◽  
Replication Control ◽  
Compatible Plasmid ◽  
Rate Limiting

ABSTRACT Plasmid R1 is a low-copy-number plasmid that is present at a level of about four or five copies per average cell. The copy number is controlled posttranscriptionally at the level of synthesis of the rate-limiting initiator protein RepA. In addition to this, R1 has an auxiliary system that derepresses a second promoter at low copy numbers, leading to increased repA mRNA synthesis. This promoter is normally switched off by a constitutively synthesized plasmid-encoded repressor protein, CopB; in cells with low copy numbers, the concentration of CopB is low and the promoter is derepressed. Here we show that the rate of loss of a Par+ derivative of the basic replicon of R1 increased about sevenfold when the cells contained a high concentration of the CopB protein formed from a compatible plasmid.

scholarly journals Multipartite Regulation of rctB, the Replication Initiator Gene of Vibrio cholerae Chromosome II

2005 ◽  
Vol 187 (21) ◽  
pp. 7167-7175 ◽  
Author(s):  
Debasish Pal ◽  
Tatiana Venkova-Canova ◽  
Preeti Srivastava ◽  
Dhruba K. Chattoraj
Keyword(s):  
Vibrio Cholerae ◽  
Copy Number ◽  
Promoter Activity ◽  
Replication Initiation ◽  
E Coli ◽  
Long Range Interactions ◽  
Replication Control ◽  
Chromosome Ii ◽  
Replication Initiator ◽  
Rate Limiting

ABSTRACT Replication initiator proteins in bacteria not only allow DNA replication but also often regulate the rate of replication initiation as well. The regulation is mediated by limiting the synthesis or availability of initiator proteins. The applicability of this principle is demonstrated here for RctB, the replication initiator for the smaller of the two chromosomes of Vibrio cholerae. A strong promoter for the rctB gene named rctBp was identified and found to be autoregulated in Escherichia coli. Promoter activity was lower in V. cholerae than in E. coli, and a part of this reduction is likely to be due to autorepression. Sequences upstream of rctBp, implicated earlier in replication control, enhanced the repression. The action of the upstream sequences required that they be present in cis, implying long-range interactions in the control of the promoter activity. A second gene specific for chromosome II replication, rctA, reduced rctB translation, most likely by antisense RNA control. Finally, optimal rctBp activity was found to be dependent on Dam. Increasing RctB in trans increased the copy number of a miniplasmid carrying oriCIIVC , implying that RctB can be rate limiting for chromosome II replication. The multiple modes of control on RctB are expected to reduce fluctuations in the initiator concentration and thereby help maintain chromosome copy number homeostasis.

scholarly journals Increased copy number couples the evolution of plasmid horizontal transmission and plasmid-encoded antibiotic resistance

2021 ◽  
Vol 118 (31) ◽  
pp. e2107818118
Author(s):  
Tatiana Dimitriu ◽  
Andrew C. Matthews ◽  
Angus Buckling
Keyword(s):  
Copy Number ◽  
Horizontal Transmission ◽  
Bacterial Host ◽  
Transfer Rates ◽  
Transmission Rates ◽  
Plasmid R1 ◽  
Copy Numbers ◽  
Selection For ◽  
High Concentrations ◽  
Plasmid Carriage

Conjugative plasmids are mobile elements that spread horizontally between bacterial hosts and often confer adaptive phenotypes, including antimicrobial resistance (AMR). Theory suggests that opportunities for horizontal transmission favor plasmids with higher transfer rates, whereas selection for plasmid carriage favors less-mobile plasmids. However, little is known about the mechanisms leading to variation in transmission rates in natural plasmids or the resultant effects on their bacterial host. We investigated the evolution of AMR plasmids confronted with different immigration rates of susceptible hosts. Plasmid RP4 did not evolve in response to the manipulations, but plasmid R1 rapidly evolved up to 1,000-fold increased transfer rates in the presence of susceptible hosts. Most evolved plasmids also conferred on their hosts the ability to grow at high concentrations of antibiotics. This was because plasmids evolved greater copy numbers as a function of mutations in the copA gene controlling plasmid replication, causing both higher transfer rates and AMR. Reciprocally, plasmids with increased conjugation rates also evolved when selecting for high levels of AMR, despite the absence of susceptible hosts. Such correlated selection between plasmid transfer and AMR could increase the spread of AMR within populations and communities.

scholarly journals Cryo-EM reconstruction of AlfA fromBacillus subtilisreveals the structure of a simplified actin-like filament at 3.4-Å resolution

2018 ◽  
Vol 115 (13) ◽  
pp. 3458-3463 ◽  
Author(s):  
Andrzej Szewczak-Harris ◽  
Jan Löwe
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Copy Number ◽  
Adaptor Protein ◽  
Nucleotide Hydrolysis ◽  
Left Handed ◽  
Plasmid R1 ◽  
Copy Number Plasmid ◽  
Centromeric Sequence ◽  
Low Copy Number

Low copy-number plasmid pLS32 ofBacillus subtilissubsp.nattocontains a partitioning system that ensures segregation of plasmid copies during cell division. The partitioning locus comprises actin-like protein AlfA, adaptor protein AlfB, and the centromeric sequenceparN. Similar to the ParMRC partitioning system fromEscherichia coliplasmid R1, AlfA filaments form actin-like double helical filaments that arrange into an antiparallel bipolar spindle, which attaches its growing ends to sister plasmids through interactions with AlfB andparN. Because, compared with ParM and other actin-like proteins, AlfA is highly diverged in sequence, we determined the atomic structure of nonbundling AlfA filaments to 3.4-Å resolution by cryo-EM. The structure reveals how the deletion of subdomain IIB of the canonical actin fold has been accommodated by unique longitudinal and lateral contacts, while still enabling formation of left-handed, double helical, polar and staggered filaments that are architecturally similar to ParM. Through cryo-EM reconstruction of bundling AlfA filaments, we obtained a pseudoatomic model of AlfA doublets: the assembly of two filaments. The filaments are antiparallel, as required by the segregation mechanism, and exactly antiphasic with near eightfold helical symmetry, to enable efficient doublet formation. The structure of AlfA filaments and doublets shows, in atomic detail, how deletion of an entire domain of the actin fold is compensated by changes to all interfaces so that the required properties of polymerization, nucleotide hydrolysis, and antiparallel doublet formation are retained to fulfill the system’s biological raison d’être.

scholarly journals Replication Control of Staphylococcal Multiresistance Plasmid pSK41: an Antisense RNA Mediates Dual-Level Regulation of Rep Expression

2006 ◽  
Vol 188 (12) ◽  
pp. 4404-4412 ◽  
Author(s):  
Stephen M. Kwong ◽  
Ronald A. Skurray ◽  
Neville Firth
Keyword(s):  
Translation Initiation ◽  
Antisense Rna ◽  
Copy Number ◽  
Translation Initiation Region ◽  
Stem Loop ◽  
Initiator Protein ◽  
Stem Loop Structure ◽  
Secondary Structure Predictions ◽  
Replication Control ◽  
Replication Initiator

ABSTRACT Replication of staphylococcal multiresistance plasmid pSK41 is negatively regulated by the antisense transcript RNAI. pSK41 minireplicons bearing rnaI promoter (P rnaI ) mutations exhibited dramatic increases in copy number, approximately 40-fold higher than the copy number for the wild-type replicon. The effects of RNAI mutations on expression of the replication initiator protein (Rep) were evaluated using transcriptional and translational fusions between the rep control region and the cat reporter gene. The results suggested that when P rnaI is disrupted, the amount of rep mRNA increases and it becomes derepressed for translation. These effects were reversed when RNAI was provided in trans, demonstrating that it is responsible for significant negative regulation at two levels, with the greatest repression exerted on rep translation initiation. Mutagenesis provided no evidence for RNAI-mediated transcriptional attenuation as a basis for the observed reduction in rep message associated with expression of RNAI. However, RNA secondary-structure predictions and supporting mutagenesis data suggest a novel mechanism for RNAI-mediated repression of rep translation initiation, where RNAI binding promotes a steric transition in the rep mRNA leader to an alternative thermodynamically stable stem-loop structure that sequesters the rep translation initiation region, thereby preventing translation.

scholarly journals Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xinping Fan ◽  
Guanghao Luo ◽  
Yu S. Huang
Keyword(s):  
Copy Number ◽  
Bayesian Learning ◽  
Kernel Smoothing ◽  
Gaussian Mixture ◽  
Copy Number Alterations ◽  
Sequencing Data ◽  
Copy Numbers ◽  
Allele Specific ◽  
Tumor Sequencing ◽  
Low Coverage

Abstract Background Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. Results We introduce Accucopy, a method to infer total copy numbers (TCNs) and allele-specific copy numbers (ASCNs) from challenging low-purity and low-coverage tumor samples. Accucopy adopts many robust statistical techniques such as kernel smoothing of coverage differentiation information to discern signals from noise and combines ideas from time-series analysis and the signal-processing field to derive a range of estimates for the period in a histogram of coverage differentiation information. Statistical learning models such as the tiered Gaussian mixture model, the expectation–maximization algorithm, and sparse Bayesian learning were customized and built into the model. Accucopy is implemented in C++ /Rust, packaged in a docker image, and supports non-human samples, more at http://www.yfish.org/software/. Conclusions We describe Accucopy, a method that can predict both TCNs and ASCNs from low-coverage low-purity tumor sequencing data. Through comparative analyses in both simulated and real-sequencing samples, we demonstrate that Accucopy is more accurate than Sclust, ABSOLUTE, and Sequenza.

Infection with antiretroviral-susceptible HIV in an individual adherent to pre-exposure prophylaxis: strategies for treatment initiation

2021 ◽  
pp. 095646242097112
Author(s):  
Jessica M Hughes ◽  
Darrell HS Tan ◽  
Peter Anderson ◽  
Janani Bodhinayake ◽  
Paul A MacPherson
Keyword(s):  
Viral Load ◽  
Copy Number ◽  
Case Reports ◽  
Pharmacy Records ◽  
Treatment Regimens ◽  
Viral Copy Number ◽  
Low Copy Number ◽  
Viral Copy ◽  
Exposure Prophylaxis ◽  
Tenofovir Diphosphate

HIV pre-exposure prophylaxis (PrEP) is effective at preventing sexual acquisition of HIV, and failures in clinical trials are largely attributable to medication nonadherence. We report here a case of infection with a fully susceptible strain of HIV in an individual adherent to PrEP as demonstrated by pharmacy records and intracellular tenofovir diphosphate levels. At diagnosis, the viral load was 90 copies/mL precluding initial genotype testing due to low copy number. While PrEP failure is rare, this case underscores the importance of regular HIV testing for patient on PrEP and prompts discussion regarding the approach to treatment following failure where an initial genotype is not yet available or not possible due to low viral load. Few other case reports of PrEP failure exist in the literature and approaches to treatment varied widely. We suggest the initial viral copy number may guide next steps and discuss the risks and benefits of stopping PrEP, escalating therapy with integrase inhibitors or boosted protease inhibitors, or switching to non-nucleoside antiretroviral treatment regimens.

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