scholarly journals Essential gene acquisition destabilizes plasmid inheritance

PLoS Genetics ◽  
2021 ◽  
Vol 17 (7) ◽  
pp. e1009656
Author(s):  
Tanita Wein ◽  
Yiqing Wang ◽  
Myriam Barz ◽  
Fenna T. Stücker ◽  
Katrin Hammerschmidt ◽  
...  
Keyword(s):  
Essential Gene ◽  
Antibiotic Resistance Genes ◽  
Essential Genes ◽  
Dose Effect ◽  
Genetic Elements ◽  
Metabolic Functions ◽  
Gene Acquisition ◽  
Gene Redundancy ◽  
Evolutionary Success ◽  
The Stability

Extra-chromosomal genetic elements are important drivers of evolutionary transformations and ecological adaptations in prokaryotes with their evolutionary success often depending on their ‘utility’ to the host. Examples are plasmids encoding antibiotic resistance genes, which are known to proliferate in the presence of antibiotics. Plasmids carrying an essential host function are recognized as permanent residents in their host. Essential plasmids have been reported in several taxa where they often encode essential metabolic functions; nonetheless, their evolution remains poorly understood. Here we show that essential genes are rarely encoded on plasmids; evolving essential plasmids in Escherichia coli we further find that acquisition of an essential chromosomal gene by a plasmid can lead to plasmid extinction. A comparative genomics analysis of Escherichia isolates reveals few plasmid-encoded essential genes, yet these are often integrated into plasmid-related functions; an example is the GroEL/GroES chaperonin. Experimental evolution of a chaperonin-encoding plasmid shows that the acquisition of an essential gene reduces plasmid fitness regardless of the stability of plasmid inheritance. Our results suggest that essential plasmid emergence leads to a dose effect caused by gene redundancy. The detrimental effect of essential gene acquisition on plasmid inheritance constitutes a barrier for plasmid-mediated lateral gene transfer and supplies a mechanistic understanding for the rarity of essential genes in extra-chromosomal genetic elements.

scholarly journals Mobile Genetic Elements Drive the Antibiotic Resistome Alteration in Freshwater Shrimp Aquaculture

Water ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1461
Author(s):  
Hao Fang ◽  
Nan Ye ◽  
Kailong Huang ◽  
Junnan Yu ◽  
Shuai Zhang
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Procambarus Clarkii ◽  
Variation Partitioning ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
Shrimp Aquaculture ◽  
Sediment Samples ◽  
Genetic Elements ◽  
Freshwater Aquaculture

Shrimp aquaculture environments are a natural reservoir of multiple antibiotic resistance genes (ARGs) due to the overuse of antibiotics. Nowadays, the prevalence of these kinds of emerging contaminants in shrimp aquaculture environments is still unclear. In this study, high-throughput sequencing techniques were used to analyze the distribution of ARGs and mobile genetic elements (MGEs), bacterial communities, and their correlations in water and sediment samples in two types of typical shrimp (Procambarus clarkii and Macrobrachium rosenbergii) freshwater aquaculture environments. A total of 318 ARG subtypes within 19 ARG types were detected in all the samples. The biodiversity and relative abundance of ARGs in sediment samples showed much higher levels compared to water samples from all ponds in the study area. Bacitracin (17.44–82.82%) and multidrug (8.57–49.70%) were dominant ARG types in P. clarkii ponds, while sulfonamide (26.33–39.59%) and bacitracin (12.75–37.11%) were dominant ARG types in M. rosenbergii ponds. Network analysis underlined the complex co-occurrence patterns between bacterial communities and ARGs. Proteobacteria, Cyanobacteria, and Actinobacteria exhibited a high abundance in all samples, in which C39 (OTU25355) and Hydrogenophaga (OTU162961) played important roles in the dissemination of and variation in ARGs based on their strong connections between ARGs and bacterial communities. Furthermore, pathogens (e.g., Aeromonadaceae (OTU195200) and Microbacteriaceae (OTU16033)), which were potential hosts for various ARGs, may accelerate the propagation of ARGs and be harmful to human health via horizontal gene transfer mediated by MGEs. Variation partitioning analysis further confirmed that MGEs were the most crucial contributor (74.76%) driving the resistome alteration. This study may help us to understand the non-ignorable correlations among ARGs, bacterial diversity, and MGEs in the shrimp freshwater aquaculture environments.

A novel way to purify recombinant baculoviruses by using bacmid

2009 ◽  
Vol 29 (2) ◽  
pp. 71-75 ◽  
Author(s):  
Wu-Jie Su ◽  
Wei-De Shen ◽  
Bing Li ◽  
Yan Wu ◽  
Guang Gao ◽  
...  
Keyword(s):  
Insect Cells ◽  
Nuclear Polyhedrosis Virus ◽  
Essential Gene ◽  
Essential Genes ◽  
Reading Frame ◽  
Recombinant Viruses ◽  
Recombinant Bacmid ◽  
Bmnpv Bacmid ◽  
Nuclear Polyhedrosis ◽  
Recombinant Bacmids

In the present study, we studied the feasibility of deleting essential genes in insect cells by using bacmid and purifying recombinant bacmid in Escherichia coli DH10B cells. To disrupt the orf4 (open reading frame 4) gene of BmNPV [Bm (Bombyx mori) nuclear polyhedrosis virus], a transfer vector was constructed and co-transfected with BmNPV bacmid into Bm cells. Three passages of viruses were carried out in Bm cells, followed by one round of purification. Subsequently, bacmid DNA was extracted and transformed into competent DH10B cells. A colony harbouring only orf4-disrupted bacmid DNA was identified by PCR. A mixture of recombinant (white colonies) and non-recombinant (blue colonies) bacmids were also transformed into DH10B cells. PCR with M13 primers showed that the recombinant and non-recombinant bacmids were separated after transformation. The result confirmed that purification of recombinant viruses could be carried out simply by transformation and indicated that this method could be used to delete essential genes. Orf4-disrupted bacmid DNA was extracted and transfected into Bm cells. Viable viruses were produced, showing that orf4 was not an essential gene.

Mercury resistance (mer) operons in enterobacteria

2002 ◽  
Vol 30 (4) ◽  
pp. 719-722 ◽  
Author(s):  
J. L. Hobman ◽  
A. M. M. Essa ◽  
N. L. Brown
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Mercury Resistance ◽  
Genetic Elements ◽  
Mercuric Ion

Mercury resistance is found in many genera of bacteria. Common amongst enterobacteria are transposons related to Tn21, which is both mercuric ion- and streptomycin-/spectinomycin-and sulphonamide-resistant. Other Tn21-related transposons often have different antibiotic resistances compared with Tn21, but share many non-antibiotic-resistance genes with it. In this article we discuss possible mechanisms for the evolution of Tn21 and related genetic elements.

scholarly journals NetGenes: A database of essential genes predicted using features from interaction networks

2020 ◽  
Author(s):  
Vimaladhasan Senthamizhan ◽  
Balaraman Ravindran ◽  
Karthik Raman
Keyword(s):  
Prediction Models ◽  
Essential Gene ◽  
Gene Prediction ◽  
High Accuracy ◽  
Essential Genes ◽  
Interaction Networks ◽  
Functional Association ◽  
String Database ◽  
Feature Vectors ◽  
Link Type

AbstractEssential gene prediction models built so far are heavily reliant on sequence-based features and the scope of network-based features has been narrow. Previous work from our group demonstrated the importance of using network-based features for predicting essential genes with high accuracy. Here, we applied our approach for the prediction of essential genes to organisms from the STRING database and hosted the results in a standalone website. Our database, NetGenes, contains essential gene predictions for 2700+ bacteria predicted using features derived from STRING protein-protein functional association networks. Housing a total of 3.5M+ genes, NetGenes offers various features like essentiality scores, annotations and feature vectors for each gene. NetGenes is available at https://rbc-dsai.iitm.github.io/NetGenes/

scholarly journals Draft Genome Sequence of the Industrially Significant Bacterium Pseudomonas fluorescens ATCC 13525

2018 ◽  
Vol 7 (17) ◽  
Author(s):  
M. J. Meier ◽  
R. M. Subasinghe ◽  
L. A. Beaudette
Keyword(s):  
Antibiotic Resistance ◽  
Pseudomonas Fluorescens ◽  
Virulence Factors ◽  
Draft Genome ◽  
Antibiotic Resistance Genes ◽  
Strain Atcc ◽  
Negative Bacterium ◽  
Gram Negative ◽  
Content Type ◽  
Metabolic Functions

Pseudomonas fluorescens is a Gram-negative bacterium with versatile metabolic functions and potential industrial uses. We sequenced P. fluorescens strain ATCC 13525 with the goal of determining virulence factors and antibiotic resistance genes to predict the potential impacts on human and environmental health in the event of exposure.

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