scholarly journals Horizontal gene transfer by natural transformation promotes both genetic and epigenetic inheritance of traits

2019 ◽  
Author(s):  
Ankur B. Dalia ◽  
Triana N. Dalia
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Dna Sequences ◽  
Natural Transformation ◽  
Temporal Dynamics ◽  
Epigenetic Inheritance ◽  
Major Mechanism ◽  
A Cell ◽  
Dna 2

AbstractNatural transformation (NT) is a major mechanism of horizontal gene transfer in microbial species that promotes the spread of antibiotic resistance determinants and virulence factors. Here, we develop a cell biological approach to characterize the spatial and temporal dynamics of homologous recombination during NT inVibrio cholerae. Our results directly demonstrate (1) that transforming DNA efficiently integrates into the genome as single-stranded DNA, (2) that the resulting heteroduplexes are resolved by chromosome replication and segregation, and (3) that integrated DNA is rapidly expressed prior to cell division. We show that the combination of these properties results in the epigenetic transfer of gene products within transformed populations, which can support the transgenerational epigenetic inheritance of antibiotic resistance in bothV. choleraeandStreptococcus pneumoniae. Thus, beyond the genetic acquisition of novel DNA sequences, NT can also promote the epigenetic inheritance of traits during this conserved mechanism of horizontal gene transfer.

scholarly journals CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Sara J. Weaver ◽  
Davi R. Ortega ◽  
Matthew H. Sazinsky ◽  
Triana N. Dalia ◽  
Ankur B. Dalia ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Vibrio Cholerae ◽  
Natural Transformation ◽  
Domain Architecture ◽  
Genetic Material ◽  
Surface Binding ◽  
Exogenous Dna ◽  
Insight Into

Abstract Natural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. In Vibrio cholerae, a type IVa pilus (T4aP) is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. Here, we use a functional tagged allele of VcPilQ purified from native V. cholerae cells to determine the cryoEM structure of the VcPilQ secretin in amphipol to ~2.7 Å. We use bioinformatics to examine the domain architecture and gene neighborhood of T4aP secretins in Proteobacteria in comparison with VcPilQ. This structure highlights differences in the architecture of the T4aP secretin from the type II and type III secretion system secretins. Based on our cryoEM structure, we design a series of mutants to reversibly regulate VcPilQ gate dynamics. These experiments support the idea of VcPilQ as a potential druggable target and provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation.

scholarly journals CryoEM structure of the Vibrio cholerae Type IV competence pilus secretin PilQ

2020 ◽  
Author(s):  
Sara J. Weaver ◽  
Matthew H. Sazinsky ◽  
Triana N. Dalia ◽  
Ankur B. Dalia ◽  
Grant J. Jensen
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Vibrio Cholerae ◽  
Natural Transformation ◽  
Structural Information ◽  
Genetic Material ◽  
Surface Binding ◽  
Exogenous Dna ◽  
Type Iv

AbstractNatural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. In Vibrio cholerae, the Type IV competence pilus is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. A lack of structural information has hindered our understanding of this process, however. Here, we solved the first ever high-resolution structure of a Type IV competence pilus secretin. A functional tagged allele of VcPilQ purified from native V. cholerae cells was used to determine the cryoEM structure of the PilQ secretin in amphipol to ∼2.7 Å. This structure highlights for the first time key differences in the architecture of the Type IV competence pilus secretin from the Type II and Type III Secretin System secretins. Based on our cryoEM structure, we designed a series of mutants to interrogate the mechanism of PilQ. These experiments provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation. We prove that it is possible to reduce pilus biogenesis and natural transformation by sealing the gate, suggesting VcPilQ as a new drug target.

scholarly journals Horizontal gene transfer facilitates the spread of extracellular antibiotic resistance genes in soil

2021 ◽  
Author(s):  
Heather A. Kittredge ◽  
Kevin M. Dougherty ◽  
Sarah E. Evans
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Resistance Genes ◽  
Natural Transformation ◽  
Antibiotic Resistance Genes ◽  
Live Cells ◽  
Resistant Bacteria ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant

AbstractAntibiotic resistance genes (ARGs) are ubiquitous in the environment and pose a serious risk to human and veterinary health. While many studies focus on the spread of live antibiotic resistant bacteria throughout the environment, it is unclear whether extracellular ARGs from dead cells can transfer to live bacteria to facilitate the evolution of antibiotic resistance in nature. Here, we inoculate antibiotic-free soil with extracellular ARGs (eARGs) from dead Pseudeononas stutzeri cells and track the evolution of antibiotic resistance via natural transformation – a mechanism of horizontal gene transfer involving the genomic integration of eARGs. We find that transformation facilitates the rapid evolution of antibiotic resistance even when eARGs occur at low concentrations (0.25 μg g-1 soil). However, when eARGs are abundant, transformation increases substantially. The evolution of antibiotic resistance was high under soil moistures typical in terrestrial systems (5%-30% gravimetric water content) and was only inhibited at very high soil moistures (>30%). While eARGs transformed into live cells at a low frequency, exposure to a low dose of antibiotic allowed a small number of transformants to reach high abundances in laboratory populations, suggesting even rare transformation events pose a risk to human health. Overall, this work demonstrates that dead bacteria and their eARGs are an overlooked path to antibiotic resistance, and that disinfection alone is insufficient to stop the spread of antibiotic resistance. More generally, the spread of eARGs in antibiotic-free soil suggests that transformation allows genetic variants to establish at low frequencies in the absence of antibiotic selection.ImportanceOver the last decade, antibiotics in the environment have gained increasing attention because they can select for drug-resistant phenotypes that would have otherwise gone extinct. To counter this effect, bacterial populations exposed to antibiotics often undergo disinfection. However, the release of extracellular antibiotic resistance genes (eARGs) into the environment following disinfection can promote the transfer of eARGs through natural transformation. This phenomenon is well-documented in wastewater and drinking water, but yet to be investigated in soil. Our results directly demonstrate that eARGs from dead bacteria are an important, but often overlooked source of antibiotic resistance in soil. We conclude that disinfection alone is insufficient to prevent the spread of ARGs. Special caution should be taken in releasing antibiotics into the environment, even if there are no live antibiotic resistant bacteria in the community, as transformation allows DNA to maintain its biological activity past microbial death.

scholarly journals Fluorescence-Based Detection of Natural Transformation in Drug-ResistantAcinetobacter baumannii

2018 ◽  
Vol 200 (19) ◽  
Author(s):  
Anne-Sophie Godeux ◽  
Agnese Lupo ◽  
Marisa Haenni ◽  
Simon Guette-Marquet ◽  
Gottfried Wilharm ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Natural Transformation ◽  
Multidrug Resistant ◽  
New Method ◽  
Content Type ◽  
Transfer Mechanisms ◽  
Multiple Antibiotics

ABSTRACTAcinetobacter baumanniiis a nosocomial agent with a high propensity for developing resistance to antibiotics. This ability relies on horizontal gene transfer mechanisms occurring in theAcinetobactergenus, including natural transformation. To study natural transformation in bacteria, the most prevalent method uses selection for the acquisition of an antibiotic resistance marker in a target chromosomal locus by the recipient cell. Most clinical isolates ofA. baumanniiare resistant to multiple antibiotics, limiting the use of such selection-based methods. Here, we report the development of a phenotypic and selection-free method based on flow cytometry to detect transformation events in multidrug-resistant (MDR) clinicalA. baumanniiisolates. To this end, we engineered a translational fusion between the abundant and conservedA. baumanniinucleoprotein (HU) and the superfolder green fluorescent protein (sfGFP). The new method was benchmarked against the conventional antibiotic selection-based method. Using this new method, we investigated several parameters affecting transformation efficiencies and identified conditions of transformability one hundred times higher than those previously reported. Using optimized transformation conditions, we probed natural transformation in a set of MDR clinical and nonclinical animalA. baumanniiisolates. Regardless of their origin, the majority of the isolates displayed natural transformability, indicative of a conserved trait in the species. Overall, this new method and optimized protocol will greatly facilitate the study of natural transformation in the opportunistic pathogenA. baumannii.IMPORTANCEAntibiotic resistance is a pressing global health concern with the rise of multiple and panresistant pathogens. The rapid and unfailing resistance to multiple antibiotics of the nosocomial agentAcinetobacter baumannii, notably to carbapenems, prompt to understand the mechanisms behind acquisition of new antibiotic resistance genes. Natural transformation, one of the horizontal gene transfer mechanisms in bacteria, was only recently described inA. baumanniiand could explain its ability to acquire resistance genes. We developed a reliable method to probe and study natural transformation mechanism inA. baumannii. More broadly, this new method based on flow cytometry will allow experimental detection and quantification of horizontal gene transfer events in multidrug-resistantA. baumannii.

scholarly journals Interbacterial transfer of carbapenem resistance and large antibiotic resistance islands by natural transformation in pathogenic Acinetobacter

2021 ◽  
Author(s):  
Anne-Sophie Godeux ◽  
Elin Svedholm ◽  
Samuel Barreto ◽  
Agnese Lupo ◽  
Marisa Haenni ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Acinetobacter Baumannii ◽  
Resistance Genes ◽  
Natural Transformation ◽  
Antibiotic Resistance Genes ◽  
Carbapenem Resistance ◽  
Predatory Behavior ◽  
Clinical Isolates

Acinetobacter baumannii infection poses a major health threat with recurrent treatment failure due to antibiotic resistance, notably to carbapenems. While genomic analyses of clinical strains indicate that homologous recombination plays a major role in the acquisition of antibiotic resistance genes, the underlying mechanisms of horizontal gene transfer often remain speculative. Our understanding of the acquisition of antibiotic resistance is hampered by the lack of experimental systems able to reproduce genomic observations. We here report the detection of recombination events occurring spontaneously in mixed bacterial populations and which can result in the acquisition of resistance to carbapenems. We show that natural transformation is the main driver of intra-, but also inter-strain recombination events between A. baumannii clinical isolates and pathogenic species of Acinetobacter. We observed that interbacterial natural transformation in mixed populations is more efficient at promoting the acquisition of large resistance islands (AbaR4, AbaR1) than providing the same bacteria with high quantities of purified genomic DNA. Importantly, analysis of the genomes of the recombinant progeny revealed large recombination tracts (from 13 to 123 kb) similar to those observed in the genome of clinical isolates. Moreover, we highlight that transforming DNA availability is a key determinant of the rate of recombination and results from both spontaneous release and interbacterial predatory behavior. Natural transformation should be considered as a leading mechanism of genome recombination and horizontal gene transfer of antibiotic resistance genes in Acinetobacter baumannii.

A kinetic model of gene transfer via natural transformation of Azotobacter vinelandii

2015 ◽  
Vol 1 (3) ◽  
pp. 363-374 ◽  
Author(s):  
Nanxi Lu ◽  
Arash Massoudieh ◽  
Xiaomeng Liang ◽  
Tamir Kamai ◽  
Julie L. Zilles ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Kinetic Model ◽  
Aquatic Environment ◽  
Natural Transformation ◽  
Azotobacter Vinelandii ◽  
Genetic Traits

Horizontal gene transfer allows antibiotic resistance and other genetic traits to spread among bacteria in the aquatic environment.

scholarly journals An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

mBio ◽  
2012 ◽  
Vol 3 (5) ◽  
Author(s):  
Peter Jorth ◽  
Marvin Whiteley
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Diversity ◽  
Natural Transformation ◽  
Bacterial Species ◽  
Comparative Genomic ◽  
Content Type ◽  
Immune Systems ◽  
Adaptive Immune ◽  
Adaptive Immune Systems

ABSTRACTNatural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history ofAggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.IMPORTANCEThe human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogenAggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competentA. actinomycetemcomitansstrains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.

scholarly journals Horizontally transferred genes in the ctenophore Mnemiopsis leidyi encode enzymes and are expressed during early development

2017 ◽  
Author(s):  
Alexandra M Hernandez ◽  
Joseph F Ryan
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Early Development ◽  
Genetic Information ◽  
Mnemiopsis Leidyi ◽  
Uncharacterized Protein ◽  
Phylogenetic Incongruence ◽  
Wide Range ◽  
Growing Body

Horizontal gene transfer has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that horizontal gene transfer (HGT) between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) appear to perform enzymatic activities in M. leidyi, supporting previous observations that enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during early development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.

scholarly journals How environment shapes horizontal gene transfer

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Rama Bhatia ◽  
Hande Kirit ◽  
Jonathan Bollback
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Dosage ◽  
Recipient Cell ◽  
Endogenous Gene ◽  
Fitness Effects ◽  
Serovar Typhimurium ◽  
A Cell ◽  
Evolutionary Fate

The evolutionary fate of a horizontal gene transfer (HGT) event is determined by its fitness on the recipient cell, i.e., whether it is beneficial, neutral or deleterious. The distribution of fitness effects (DFE), thus is a fundamental predictor of the outcome of an HGT event. The environment plays a considerable role in determining the fitness cost of a horizontally transferred gene. We have studied the fitness effects of genes transferred from Salmonella enterica serovar Typhimurium to Escherichia coli in six environments, that potentially represent the conditions experienced by the two species. The data suggests high variability of genes in different environments. Genes, whose fitness varies substantially between environments, may be able to persist in populations while being deleterious in one environment, they may be neutral or even beneficial in another environment, suggesting that environmental fluctuations may increase the likelihood of HGT. In addition to the in vitro environments, we are also looking at, how changes in the intrinsic environment of a cell, after an HGT event, could affect fitness. An increase in protein dosage due to functional similarity of the horizontally transferred gene to the endogenous gene can cause an imbalance in the cell, thereby leading to a negative fitness effect. By comparing the growth rates of each ortholog gene with the wild type strain, we can elucidate when gene dosage acts as a barrier to HGT.

scholarly journals Organization of lin Genes and IS6100 among Different Strains of Hexachlorocyclohexane-Degrading Sphingomonas paucimobilis: Evidence for Horizontal Gene Transfer

2004 ◽  
Vol 186 (8) ◽  
pp. 2225-2235 ◽  
Author(s):  
Charu Dogra ◽  
Vishakha Raina ◽  
Rinku Pal ◽  
Mrutyunjay Suar ◽  
Sukanya Lal ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Dna Sequences ◽  
Dna Hybridization ◽  
Gene Organization ◽  
Mycobacterium Fortuitum ◽  
Sphingomonas Paucimobilis ◽  
Hybridization Data ◽  
Different Strains ◽  
Geographical Locations

ABSTRACT The organization of lin genes and IS6100 was studied in three strains of Sphingomonas paucimobilis (B90A, Sp+, and UT26) which degraded hexachlorocyclohexane (HCH) isomers but which had been isolated at different geographical locations. DNA-DNA hybridization data revealed that most of the lin genes in these strains were associated with IS6100, an insertion sequence classified in the IS6 family and initially found in Mycobacterium fortuitum. Eleven, six, and five copies of IS6100 were detected in B90A, Sp+, and UT26, respectively. IS6100 elements in B90A were sequenced from five, one, and one regions of the genomes of B90A, Sp+, and UT26, respectively, and were found to be identical. DNA-DNA hybridization and DNA sequencing of cosmid clones also revealed that S. paucimobilis B90A contains three and two copies of linX and linA, respectively, compared to only one copy of these genes in strains Sp+ and UT26. Although the copy number and the sequence of the remaining genes of the HCH degradative pathway (linB, linC, linD, and linE) were nearly the same in all strains, there were striking differences in the organization of the linA genes as a result of replacement of portions of DNA sequences by IS6100, which gave them a strange mosaic configuration. Spontaneous deletion of linD and linE from B90A and of linA from Sp+ occurred and was associated either with deletion of a copy of IS6100 or changes in IS6100 profiles. The evidence gathered in this study, coupled with the observation that the G+C contents of the linA genes are lower than that of the remaining DNA sequence of S. paucimobilis, strongly suggests that all these strains acquired the linA gene through horizontal gene transfer mediated by IS6100. The association of IS6100 with the rest of the lin genes further suggests that IS6100 played a role in shaping the current lin gene organization.

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