scholarly journals Evolutionary rescue and drug resistance on multicopy plasmids

2019 ◽  
Author(s):  
Mario Santer ◽  
Hildegard Uecker
Keyword(s):  
Copy Number ◽  
Gene Dosage ◽  
Branching Processes ◽  
Plasmid Copy Number ◽  
Wild Type ◽  
Plasmid Copy ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Evolutionary Rescue ◽  
Establishment Probability

AbstractBacteria often carry “extra DNA” in form of plasmids in addition to their chromosome. Many plasmids have a copy number greater than one such that the genes encoded on these plasmids are present in multiple copies per cell. This has evolutionary consequences by increasing the mutational target size, by prompting the (transitory) co-occurrence of mutant and wild-type alleles within the same cell, and by allowing for gene dosage effects. We develop and analyze a mathematical model for bacterial adaptation to harsh environmental change if adaptation is driven by beneficial alleles on multicopy plasmids. Successful adaptation depends on the availability of advantageous alleles and on their establishment probability. The establishment process involves the segregation of mutant and wild-type plasmids to the two daughter cells, allowing for the emergence of mutant-homozygous cells over the course of several generations. To model this process, we use the theory of multi-type branching processes, where a type is defined by the genetic composition of the cell. Both factors – the number of adaptive alleles and their establishment probability – depend on the plasmid copy number, and they often do so antagonistically. We find that in the interplay of various effects, a lower or higher copy number may maximize the probability of evolutionary rescue. The decisive factor is the dominance relationship between mutant and wild-type plasmids and potential gene dosage effects. Results from a simple model of antibiotic degradation indicate that the optimal plasmid copy number may depend on the specific environment encountered by the population.

scholarly journals Evolutionary Rescue and Drug Resistance on Multicopy Plasmids

Genetics ◽  
2020 ◽  
Vol 215 (3) ◽  
pp. 847-868
Author(s):  
Mario Santer ◽  
Hildegard Uecker
Keyword(s):  
Copy Number ◽  
Gene Dosage ◽  
Branching Processes ◽  
Plasmid Copy Number ◽  
Wild Type ◽  
Plasmid Copy ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Evolutionary Rescue ◽  
Establishment Probability

Bacteria often carry “extra DNA” in the form of plasmids in addition to their chromosome. Many plasmids have a copy number greater than one such that the genes encoded on these plasmids are present in multiple copies per cell. This has evolutionary consequences by increasing the mutational target size, by prompting the (transitory) co-occurrence of mutant and wild-type alleles within the same cell, and by allowing for gene dosage effects. We develop and analyze a mathematical model for bacterial adaptation to harsh environmental change if adaptation is driven by beneficial alleles on multicopy plasmids. Successful adaptation depends on the availability of advantageous alleles and on their establishment probability. The establishment process involves the segregation of mutant and wild-type plasmids to the two daughter cells, allowing for the emergence of mutant homozygous cells over the course of several generations. To model this process, we use the theory of multitype branching processes, where a type is defined by the genetic composition of the cell. Both factors—the availability of advantageous alleles and their establishment probability—depend on the plasmid copy number, and they often do so antagonistically. We find that in the interplay of various effects, a lower or higher copy number may maximize the probability of evolutionary rescue. The decisive factor is the dominance relationship between mutant and wild-type plasmids and potential gene dosage effects. Results from a simple model of antibiotic degradation indicate that the optimal plasmid copy number may depend on the specific environment encountered by the population.

Reflections on studies of gene expression in aneuploids

2010 ◽  
Vol 426 (2) ◽  
pp. 119-123 ◽  
Author(s):  
James A. Birchler
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Gene Dosage ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Different Types ◽  
Chromosomal Copy Number ◽  
Cancerous Cells ◽  
Insight Into ◽  
Careful Documentation

Aneuploidy involves changes in chromosomal copy number compared with normal euploid genotypes. Studies of gene expression in aneuploids in a variety of species have claimed many different types of responses. Studies of individual genes suggest that there are both structural gene dosage effects and compensation in aneuploids, and that subtle trans-acting effects across the genome are quite prevalent. A discussion is presented concerning the normalization procedures for studying gene expression in aneuploids. A careful documentation of the modulations of gene expression in aneuploids should provide insight into the nature of cancerous cells and the basis of aneuploid syndromes.

scholarly journals RepB C-terminus mutation of an ori pRi vector affects plasmid copy number inAgrobacteriumand transgene copy number in plants

2018 ◽  
Author(s):  
Zarir Vaghchhipawala ◽  
Sharon Radke ◽  
Ervin Nagy ◽  
Mary L. Russell ◽  
Susan Johnson ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Copy Number ◽  
Binary Vector ◽  
Single Copy ◽  
Plasmid Copy Number ◽  
Plant Production ◽  
Silent Mutation ◽  
Wild Type ◽  
Plasmid Copy ◽  
C Terminus

AbstractA nativerepABCreplication origin, ori pRi, was previously reported as a single copy plasmid inAgrobacterium tumefaciensand can improve the production of transgenic plants with a single copy insertion of transgenes when it is used in binary vectors forAgrobacterium-mediatedtransformation. A high copy ori pRi variant plasmid, pTF::Ri, which does not improve the frequency of single copy transgenic plants, has been reported in the literature. Sequencing the high copy pTF::RirepABCoperon revealed the presence of two mutations: one silent mutation and one missense mutation that changes a tyrosine to a histidine (Y299H) in a highly conserved area of the C-terminus of the RepB protein (RepBY299H). Reproducing these mutations in the wild-type oriRi binary vector showed thatAgrobacteriumcells with the RepBY299Hmutation grow faster on both solidified and in liquid medium, and have higher plasmid copy number as determined by ddPCR. In order to investigate the impact of the RepBY299Hmutation on transformation and quality plant production, the RepBY299Hmutated ori pRi binary vector was compared with the original wild-type ori pRi binary vector and a multi-copy oriV binary vector in canola transformation. Molecular analyses of the canola transgenic plants demonstrated that the multi-copy ori pRi with the RepBY299Hmutation inAgrobacteriumcells lost the advantage of generating high frequency single copy, backbone-free transgenic plants compared to using the single copy wild-type ori pRi binary vector.

scholarly journals Spatiotemporal Variations in Growth Rate and Virulence Plasmid Copy Number during Yersinia pseudotuberculosis Infection

2021 ◽  
Author(s):  
Stephan Schneiders ◽  
Tifaine Hechard ◽  
Tomas Edgren ◽  
Kemal Avican ◽  
Maria Fällman ◽  
...  
Keyword(s):  
Growth Rates ◽  
Copy Number ◽  
Yersinia Pseudotuberculosis ◽  
Gene Dosage ◽  
Growth Dynamics ◽  
Digital Pcr ◽  
Plasmid Copy Number ◽  
Virulence Plasmid ◽  
Mesenteric Lymph Nodes ◽  
Plasmid Copy

Pathogenic Yersinia spp. depend on the activity of a potent virulence plasmid-encoded ysc/yop type 3 secretion system (T3SS) to colonize hosts and cause disease. It was recently shown that Y. pseudotuberculosis up-regulates the virulence plasmid copy number (PCN) during infection and the resulting elevated gene dose of plasmid-encoded T3SS genes is essential for virulence. When and how this novel regulatory mechanism is deployed and regulates the replication of the virulence plasmid during infection is unknown. In the current study, we applied droplet digital PCR (ddPCR) to investigate the dynamics of Y. pseudotuberculosis virulence PCN variations and growth rates in infected mouse organs. We demonstrated that both PCN and growth varied in different tissues and over time throughout the course of infection, indicating that the bacteria adapted to discrete microenvironments during infection. The PCN was highest in Peyer’s Patches and caecum during the clonal invasive phase of the infection, while the fastest growth rates were found in the draining mesenteric lymph nodes. In deeper, systemic organs, the PCN was lower and more modest growth rates were recorded. Our study indicates that increased gene dosage of the plasmid-encoded T3SS genes is most important early in the infection during invasion of the host. The described ddPCR approach will greatly simplify analyses of PCN, growth dynamics, and bacterial loads in infected tissues, and will be readily applicable to other infection models.

scholarly journals Restoration of wild-type motility to flagellin-knockout Escherichia coli

2019 ◽  
Author(s):  
Nicholas M. Thomson ◽  
Mark J. Pallen
Keyword(s):  
Escherichia Coli ◽  
Copy Number ◽  
Plasmid Copy Number ◽  
Major Constituent ◽  
Strongly Correlated ◽  
Wild Type ◽  
Plasmid Copy ◽  
Inducible Promoters ◽  
E Coli ◽  
Flagellar Filament

AbstractFlagellin is the major constituent of the flagellar filament and faithful restoration of wild-type motility to flagellin mutants may be beneficial for studies of flagellar biology and biotechnological exploitation of the flagellar system. Therefore, we explored the restoration of motility by flagellin expressed from a variety of combinations of promoter, plasmid copy number and induction strength. Motility was only partially restored using the tightly regulated rhamnose promoter, but wild-type motility was achieved with the T5 promoter, which, although leaky, allowed titration of induction strength. Motility was little affected by plasmid copy number when dependent on inducible promoters. However, plasmid copy number was important when expression was controlled by the native E. coli flagellin promoter. Motility was poorly correlated with flagellin transcription levels, but strongly correlated with the amount of flagellin associated with the flagellar filament, suggesting that excess monomers are either not exported or not assembled into filaments. This study provides a useful reference for further studies of flagellar function and a simple blueprint for similar studies with other proteins.

scholarly journals Oligogenic effects of 16p11.2 copy number variation on craniofacial development

2019 ◽  
Author(s):  
Yuqi Qiu ◽  
Thomas Arbogast ◽  
Sandra Martin Lorenzo ◽  
Honying Li ◽  
Shih C. Tang ◽  
...  
Keyword(s):  
Copy Number ◽  
Gene Dosage ◽  
Copy Number Variant ◽  
Craniofacial Development ◽  
Model Organisms ◽  
List Type ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Craniofacial Structure ◽  
Mirror Effects

AbstractA copy number variant (CNV) of 16p11.2, which encompasses 30 genes, is associated with developmental and psychiatric disorders, head size and body mass. The genetic mechanisms that underlie these associations are not understood. To elucidate the effects of genes on development, we exploited the quantitative effects of CNV on craniofacial structure in humans and model organisms. We show that reciprocal deletion and duplication of 16p11.2 have characteristic “mirror” effects on craniofacial features that are conserved in human, rat and mouse. By testing gene dosage effects on the shape of the mandible in zebrafish, we show that the distribution of effects for all individual genes is consistent with that of the CNV, and some combinations have non-additive effects. Our results suggest that, at minimum, one third of genes within the 16p11.2 region influence craniofacial development, and the facial gestalt of each CNV represents a product of 30 dosage effects.HighlightsReciprocal CNVs of 16p11.2 have mirror effects on craniofacial structure. Copy number is associated with a positive effect on nasal and mandibular regions and a negative effect on frontal regions of the face.Effects of CNV on craniofacial development in human are well conserved in rat and mouse models of 16p11.2 deletion and duplication.7/30 genes each independently have significant effects on the shape of the mandible in zebrafish; these include SPN, C16orf54, SEZ6L2, ASPHD1, TAOK2, INO80E and FAM57B. Others (MAPK3, MVP, KCTD13) have detectable effects only in combination.Overexpression of 30 genes individually showed a distribution of effects that was skewed in the same direction as that of the full duplication, suggesting that specific facial features represent the net of all individual effects combined.

scholarly journals Selection of SHV Extended-Spectrum-β-Lactamase-Dependent Cefotaxime and Ceftazidime Resistance in Klebsiella pneumoniae Requires a Plasmid-Borne blaSHV Gene

2007 ◽  
Vol 52 (2) ◽  
pp. 441-445 ◽  
Author(s):  
David S. Hammond ◽  
Tegan Harris ◽  
Jan Bell ◽  
John Turnidge ◽  
Philip M. Giffard
Keyword(s):  
Klebsiella Pneumoniae ◽  
Copy Number ◽  
Gene Dosage ◽  
Single Cells ◽  
The Other ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Extended Spectrum ◽  
Copy Number Amplification ◽  
Selection Of

ABSTRACT In Klebsiella pneumoniae, it is common for plasmid-located and chromosome-located bla SHV copies to coexist within single cells. The plasmid-borne genes are mainly derived from two separate IS26-mediated mobilizations of bla SHV. The objective of this study was to test the hypothesis that the presence of a non-extended-spectrum β-lactamase (non-ESBL) encoding plasmid-borne form of bla SHV facilitates the cefotaxime (CTX)-mediated selection of ESBL-expressing mutants, even when there is a chromosomal copy of the same gene. Twenty-one diverse ESBL-negative, bla TEM-negative K. pneumoniae clinical isolates were tested for the IS26 insertions characteristic of the two mobilization events. The isolates were then tested for their ability to be selected for ESBL-mediated CTX resistance by serial subculturing with a doubling of the CTX concentration at every subculture. Fourteen isolates possessed neither of the IS26 insertions. None of these became ESBL positive, and all died during the course of the experiment, despite possessing chromosomal bla SHV copies. The other isolates all became ESBL positive and grew abundantly up to a CTX concentration of 128 μg/ml. Similar results were obtained with ceftazidime. ESBL expression was associated with the appearance of the expected G→A mutation at position 1 of codon 238 and also with bla SHV copy number amplification. It was concluded that plasmid-borne bla SHV greatly facilitates the selection of ESBL expression, even when the same gene is on the chromosome, and that gene dosage effects are likely to contribute to this phenomenon.

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