Natural DNA Uptake by Escherichia coli

Sinha, Sunita; Redfield, Rosemary J.

doi:10.1371/journal.pone.0035620

Cited by 45 publications

(43 citation statements)

References 61 publications

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“…A number of pathogens harboring T4P, including Pseudomonas aeruginosa and enterohemorrhagic E. coli (EHEC), are highly suspicious of being competent given the excessive HGT documented for their genomes, but to date they have not been shown to undergo transformation naturally (55)(56)(57). Our finding that the comEC mutants are attenuated in the Galleria mellonella infection model while the pilT mutants are not is unexpected.…”

Section: Discussionmentioning

confidence: 72%

DNA Uptake by the Nosocomial Pathogen Acinetobacter baumannii Occurs during Movement along Wet Surfaces

Wilharm¹,

Piesker²,

Laue³

et al. 2013

Journal of Bacteriology

114

165

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bThe emergence of Acinetobacter baumannii as an increasingly multidrug-resistant nosocomial pathogen largely relies on acquisition of resistance genes via horizontal gene transfer. Here, we demonstrate that many clinical isolates of A. baumannii take up DNA while they move along wet surfaces. We show that both motility and DNA uptake are abolished after inactivation of pilT, which putatively encodes the type 4 pilus (T4P) retraction ATPase, and comEC, which putatively encodes the DNA uptake channel, respectively. Inactivation of pilT correlates with an increase in the number and length of pili with an average diameter of 7.2 nm. In the Galleria mellonella infection model, the comEC mutant is significantly attenuated, whereas the pilT mutant is not, dissecting biologically distinct roles of T4P and the DNA uptake channel. Collectively, these findings promote our understanding of the mechanisms of DNA uptake and resistance development in A. baumannii, which may also apply to other important pathogens.

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Section: Discussionmentioning

confidence: 72%

DNA Uptake by the Nosocomial Pathogen Acinetobacter baumannii Occurs during Movement along Wet Surfaces

Wilharm¹,

Piesker²,

Laue³

et al. 2013

Journal of Bacteriology

114

165

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“…has shown that competence induction also depends on quorum sensing, pyrimidine precursors, and the presence of chitin breakdown products generated from crustacean exoskeletons (38)(39)(40)(41)(42). Although Escherichia coli's competence gene homologs enable cells to use DNA as a sole source of carbon, attempts to demonstrate natural competence in E. coli have not been successful (43,44). Less is known about regulatory mechanisms in other Gram-negative species, since culture conditions that induce competence have not been linked to specific regulators (4,45).…”

Section: The Mechanism and Function Of Natural Competencementioning

confidence: 99%

Natural Competence and the Evolution of DNA Uptake Specificity

2014

Self Cite

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Many bacteria are naturally competent, able to actively transport environmental DNA fragments across their cell envelope and into their cytoplasm. Because incoming DNA fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular DNA. This review starts with an introductory overview of competence and continues with a detailed consideration of the DNA uptake specificity of competent proteobacteria in the Pasteurellaceae and Neisseriaceae. Species in these distantly related families exhibit strong preferences for genomic DNA from close relatives, a self-specificity arising from the combined effects of biases in the uptake machinery and genomic overrepresentation of the sequences this machinery prefers. Other competent species tested lack obvious uptake bias or uptake sequences, suggesting that strong convergent evolutionary forces have acted on these two families. Recent results show that uptake sequences have multiple "dialects," with clades within each family preferring distinct sequence variants and having corresponding variants enriched in their genomes. Although the genomic consensus uptake sequences are 12 and 29 to 34 bp, uptake assays have found that only central cores of 3 to 4 bp, conserved across dialects, are crucial for uptake. The other bases, which differ between dialects, make weaker individual contributions but have important cooperative interactions. Together, these results make predictions about the mechanism of DNA uptake across the outer membrane, supporting a model for the evolutionary accumulation and stability of uptake sequences and suggesting that uptake biases may be more widespread than currently thought. N aturally competent bacteria actively pull DNA fragments from their environment into their cells. These fragments provide nucleotides, but high similarity with the chromosome also allows them to change the cell's genotype by homologous recombination, a process called natural transformation ( Fig. 1; reviewed in references 1, 2, 3, 4, and 5). Most competent bacteria that have been tested can take up DNA from any source, but species in two distantly related families of Gram-negative bacteria, the Pasteurellaceae and the Neisseriaceae, show strong preferences for DNAs containing short sequences that are highly overrepresented in their own genomes, leading to preferential uptake of conspecific DNA (6). This self-specificity both raises questions about and provides a tool for investigating the evolution of competence and the mechanism of DNA uptake.We begin with a general overview of competence, emphasizing the evolutionary issues. We then describe the two components that together create self-specificity, sequence biases in the DNA uptake machinery and overrepresentation of uptake sequences in the genomes, highlighting recent work on the mechanism and evolution of uptake biases in the two families and an evolutionary model that accounts for upt...

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“…antibiotics. E. coli is one of the Gram-negative bacteria that is naturally competent for transformation [43,44], but the competence is time limited [45]. Again, a longer contact time will increase the probability of uptake.…”

Section: Antibiotic Resistance Induction In Wwtpmentioning

confidence: 99%

Effect of Sedimentation and Aeration on Antibiotic Resistance Induction in the Activated Sludge Process

Sulfikar

Honda

Noguchi

et al. 2018

J. of Wat. & Envir. Tech.

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The influent of municipal wastewater treatment plants (WWTP) can contain micropollutants such as antibiotics, chlorine, detergents, and biocides. In vitro studies have shown that these micropollutants may induce antibiotic resistance in bacteria. Previous studies have reported increases or decreases of antibiotic-resistant bacteria between the influent and effluent of WWTP in an unpredictable manner. Thus, the triggers of resistance induction in WWTP are largely unknown. To investigate the effects of unit operations in WWTP on antibiotic resistance induction, we incubated sixteen strains of Escherichia coli susceptible to amoxicillin or norfloxacin under simulated conditions of the primary sedimentation tank, aeration tank and final sedimentation tank in sterilized and filtered wastewater from each tank at 25°C for 1, 6 and 2 hours, respectively, which are typical hydraulic retention time of each tank. The minimum inhibition concentration towards amoxicillin or norfloxacin was compared before and after incubation to evaluate the occurrence of induction. We found that resistance to both antibiotics was more likely to increase in the aeration tank than in the primary sedimentation tank or final sedimentation tank. The longer contact time with the wastewater and the aeration are factors that appeared to induce antibiotic resistance in an activated sludge process.

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Natural DNA Uptake by Escherichia coli

Cited by 45 publications

References 61 publications

DNA Uptake by the Nosocomial Pathogen Acinetobacter baumannii Occurs during Movement along Wet Surfaces

DNA Uptake by the Nosocomial Pathogen Acinetobacter baumannii Occurs during Movement along Wet Surfaces

Natural Competence and the Evolution of DNA Uptake Specificity

Effect of Sedimentation and Aeration on Antibiotic Resistance Induction in the Activated Sludge Process

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