The DNA-Uptake Process of Naturally Competent Vibrio cholerae

Matthey, Noémie; Blokesch, Melanie

doi:10.1016/j.tim.2015.10.008

Cited by 65 publications

(64 citation statements)

References 104 publications

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“…Natural transformation is a major mechanism of horizontal gene transfer (HGT) and plays a prominent role in bacterial evolution [39]. The process of Vibrio cholerae natural transformation involves four steps: DNA-binding via type IV pili, DNA pulling via ComEA, DNA translocation via ComEC, and DNA recombination by the single-strand DNA-binding proteins DprA and RecA [40]. Previously, we found that R. anatipestifer CH-1 is naturally competent [41].…”

Section: Resultsmentioning

confidence: 99%

Identifying the Genes Responsible for Iron-Limited Condition in Riemerella anatipestifer CH-1 through RNA-Seq-Based Analysis

Liu

Zhu

et al. 2017

BioMed Research International

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One of the important elements for most bacterial growth is iron, the bioavailability of which is limited in hosts. Riemerella anatipestifer (R. anatipestifer, RA), an important duck pathogen, requires iron to live. However, the genes involved in iron metabolism and the mechanisms of iron transport are largely unknown. Here, we investigated the transcriptomic effects of iron limitation condition on R. anatipestifer CH-1 using the RNA-Seq and RNA-Seq-based analysis. Data analysis revealed genes encoding functions related to iron homeostasis, including a number of putative TonB-dependent receptor systems, a HmuY-like protein-dependent hemin (an iron-containing porphyrin) uptake system, a Feo system, a gene cluster related to starch utilization, and genes encoding hypothetical proteins that were significantly upregulated in response to iron limitation. Compared to the number of upregulated genes, more genes were significantly downregulated in response to iron limitation. The downregulated genes mainly encoded a number of outer membrane receptors, DNA-binding proteins, phage-related proteins, and many hypothetical proteins. This information suggested that RNA-Seq-based analysis in iron-limited medium is an effective and fast method for identifying genes involved in iron uptake in R. anatipestifer CH-1.

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Section: Resultsmentioning

confidence: 99%

Identifying the Genes Responsible for Iron-Limited Condition in Riemerella anatipestifer CH-1 through RNA-Seq-Based Analysis

Liu

Zhu

et al. 2017

BioMed Research International

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“…Two major scenarios have been proposed. First, the T4P "fishes" for DNA at the extracellular side and by retraction through depolymerization, it takes the DNA along into the periplasm (5,6,43). Extended competence-associated T4P polymers have been found in Streptococcus pneumoniae and Vibrio cholerae but not in B. subtilis (27,44,45).…”

Section: Discussionmentioning

confidence: 99%

Kinetics of DNA uptake during transformation provide evidence for a translocation ratchet mechanism

Hepp

Maier

2016

Proc. Natl. Acad. Sci. U.S.A.

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Horizontal gene transfer can speed up adaptive evolution and support chromosomal DNA repair. A particularly widespread mechanism of gene transfer is transformation. The initial step to transformation, namely the uptake of DNA from the environment, is supported by the type IV pilus system in most species. However, the molecular mechanism of DNA uptake remains elusive. Here, we used singlemolecule techniques for characterizing the force-dependent velocity of DNA uptake by Neisseria gonorrhoeae. We found that the DNA uptake velocity depends on the concentration of the periplasmic DNA-binding protein ComE, indicating that ComE is directly involved in the uptake process. The velocity-force relation of DNA uptake is in very good agreement with a translocation ratchet model where binding of chaperones in the periplasm biases DNA diffusion through a membrane pore in the direction of uptake. The model yields a speed of DNA uptake of 900 bp·s −1 and a reversal force of 17 pN. Moreover, by comparing the velocityforce relation of DNA uptake and type IV pilus retraction, we can exclude pilus retraction as a mechanism for DNA uptake. In conclusion, our data strongly support the model of a translocation ratchet with ComE acting as a ratcheting chaperone.

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“…The principal difficulty in observing natural competence in new species is probably related to the highly disparate signals required to trigger competence gene expression. In most species, natural competence is transient and stringently regulated by secreted signal molecules and/or very specific environmental cues, such as chitin polymers in the case of Vibrio natural competence (Seitz and Blokesch, 2013; Fontaine et al, 2015; Matthey and Blokesch, 2016). While the signals triggering competence development can be highly species- and/or strain-specific, the competence machinery itself is quite similar among naturally competent bacteria, with most identified DNA uptake loci containing genes homologous to type II secretion systems (T2SS) as well as homologs of genes required for type IV pilin biogenesis (Averhoff and Friedrich, 2003; Chen and Dubnau, 2003, 2004).…”

Section: Introductionmentioning

confidence: 99%

Natural Competence Is Common among Clinical Isolates of Veillonella parvula and Is Useful for Genetic Manipulation of This Key Member of the Oral Microbiome

Knapp

Brodal

Peterson

et al. 2017

Front. Cell. Infect. Microbiol.

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The six Veillonella species found in the human oral cavity are among the most abundant members of the oral flora, occurring in both supra- and subgingival dental plaque as well as on the oral mucosa. Epidemiological data have also implicated these species in the development of the most common oral diseases. Despite their ubiquity, abundance, and ecological significance, surprisingly little is known about Veillonella biology, largely due to the difficulties associated with their genetic manipulation. In an effort to improve genetic analyses of Veillonella species, we isolated a collection of veillonellae from clinical plaque samples and screened for natural competence using a newly developed transformation protocol. Numerous strains of V. parvula were found to exhibit a natural competence ability that was highly influenced by growth medium composition. By exploiting this ability, we were able to utilize cloning-independent allelic exchange mutagenesis to identify the likely source of DNA uptake machinery within a locus homologous to type II secretion systems (T2SS). Interestingly, V. parvula natural competence was found to exhibit a clear hierarchy of preference for different sources of DNA (plasmid < PCR product < genomic DNA), which is unlike most naturally competent species. Genomic comparisons with other members of the Veillonellaceae family suggest that natural competence is likely to be widely distributed within this group. To the best of our knowledge, this study is the first demonstration of natural competence and targeted allelic exchange mutagenesis within the entire Veillonellaceae family and demonstrates a simple and rapid method to study Veillonella genetics.

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The DNA-Uptake Process of Naturally Competent Vibrio cholerae

Cited by 65 publications

References 104 publications

Identifying the Genes Responsible for Iron-Limited Condition in Riemerella anatipestifer CH-1 through RNA-Seq-Based Analysis

Identifying the Genes Responsible for Iron-Limited Condition in Riemerella anatipestifer CH-1 through RNA-Seq-Based Analysis

Kinetics of DNA uptake during transformation provide evidence for a translocation ratchet mechanism

Natural Competence Is Common among Clinical Isolates of Veillonella parvula and Is Useful for Genetic Manipulation of This Key Member of the Oral Microbiome

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