RecA and DNA recombination: a review of molecular mechanisms.

Recombinases are responsible for homologous recombination and maintenance of genome integrity. In Escherichia coli, the recombinase RecA forms a nucleoprotein filament with the ssDNA present at a DNA break and searches for a homologous dsDNA to use as a template for break repair. During the first step of this process, the ssDNA is bound to RecA and stretched into a Watson-Crick base-paired triplet conformation. The RecA nucleoprotein filament also contains ATP and Mg2+, two cofactors required for RecA activity. Then, the complex starts a homology search by interacting with and stretching dsDNA. Thanks to supercoiling, intersegment sampling and RecA clustering, a genome-wide homology search takes place at a relevant metabolic timescale. When a region of homology 8-20 base pairs in length is found and stabilized, DNA strand exchange proceeds, forming a heteroduplex complex that is resolved through a combination of DNA synthesis, ligation and resolution. RecA activities can take place without ATP hydrolysis, but this latter activity is necessary to improve and accelerate the process. Protein flexibility and monomer-monomer interactions are fundamental for RecA activity, which functions cooperatively. A structure/function relationship analysis suggests that the recombinogenic activity can be improved and that recombinases have an inherently large recombination potential. Understanding this relationship is essential for designing RecA derivatives with enhanced activity for biotechnology applications. For example, this protein is a major actor in the recombinase polymerase isothermal amplification (RPA) used in point-of-care diagnostics.

Usefulness of pan-fungal NASBA test for surveillance of environmental fungal contamination in a protected hematology unit.

A pan-fungal nucleic acid sequence based applification (NASBA) test was adapted and used for the first time to detect and quantify the level of filamentous fungi in environmental samples. Surface samples (n = 356) collected in a controlled air flow hematology ward were tested by mycological culture and the pan-fungal NASBA test. The overall percentage of agreement between culture and NASBA was 88%, the Kappa coefficient was equal to 0.61 (95%CI = [0.51; 0.72]). This pan-fungal NASBA test could be a promising tool to rapidly monitor the absence of molds in controlled environments.

Design and comparative characterization of RecA variants.

RecA plays a central role in DNA repair and is a main actor involved in recombination and activation of the SOS response. It is also used in the context of biotechnological applications in recombinase polymerase isothermal amplification (RPA). In this work, we studied the biological properties of seven RecA variants, in particular their recombinogenic activity and their ability to induce the SOS response, to better understand the structure-function relationship of RecA and the effect of combined mutations. We also investigated the biochemical properties of RecA variants that may be useful for the development of biotechnological applications. We showed that Dickeya dadantii RecA (DdRecA) had an optimum strand exchange activity at 30 °C and in the presence of a dNTP mixture that inhibited Escherichia coli RecA (EcRecA). The differences between the CTD and C-tail of the EcRecA and DdRecA domains could explain the altered behaviour of DdRecA. D. radiodurans RecA (DrRecA) was unable to perform recombination and activation of the SOS response in an E. coli context, probably due to its inability to interact with E. coli recombination accessory proteins and SOS LexA repressor. DrRecA strand exchange activity was totally inhibited in the presence of chloride ions but worked well in acetate buffer. The overproduction of Pseudomonas aeruginosa RecA (PaRecA) in an E. coli context was responsible for a higher SOS response and defects in cellular growth. PaRecA was less inhibited by the dNTP mixture than EcRecA. Finally, the study of three variants, namely, EcPa, EcRecAV1 and EcRecAV2, that contained a combination of mutations that, taken independently, are described as improving recombination, led us to raise new hypotheses on the structure-function relationship and on the monomer-monomer interactions that perturb the activity of the protein as a whole.

Detection of single-nucleotide polymorphisms in cancer-related genes by minisequencing on a microelectronic DNA chip.

The ability to realize simultaneous genotyping of multiple single-nucleotide polymorphisms or mutations is valuable in DNA samples from complex multigenic pathologies such as cancer. In this way, the complexity (number of hybridization units per chip) of the developed MICAM DNA chip, and the orientation of the grafted pyrrole oligonucleotides, make it particularly well adapted to the analysis of single-nucleotide polymorphisms/mutations in multiple potential tumoral markers. The proposed genotyping methodology is based on solid-phase minisequencing, where oligonucleotides are designed to anneal immediately upstream of the polymorphism sites, and labeled dideoxynucleotides are used as substrates for polymerase extension. The developed assay was applied to the analysis of the TP53 codon 72 polymorphism on DNA from cell lines and human colorectal samples.

Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS.

On the ISS, as on Earth, water is an essential element for life and its quality control on a regular basis allows to ensure the health of the crew and the integrity of equipment. Currently, microbial water analysis onboard ISS still relies on the traditional culture-based microbiology methods. Molecular methods based on the amplification of nucleic acids for microbiological analysis of water quality show enormous potential and are considered as the best alternative to culture-based methods. For this reason, the Midass, a fully integrated and automated prototype was designed conjointly by ESA and bioMérieux for a rapid monitoring of the microbiological quality of air. The prototype allows air sampling, sample processing and the amplification/detection of nucleic acids. We describe herein the proof of principle of an analytical approach based on molecular biology that could fulfill the ESA's need for a rapid monitoring of the microbiological quality of recycled water onboard ISS. Both concentration and recovery of microorganisms are the main critical steps when the microfiltration technology is used for water analysis. Among filters recommended standards for monitoring the microbiological quality of the water, the polycarbonate filter was fully in line with the requirements of the ISO 7704-1985 standard in terms of efficacy of capture and recovery of bacteria. Moreover, this filter does not retain nucleic acids on the surface and has no inhibitory effect on their downstream processing steps such as purification and amplification/detection. Although the Midass system was designed for the treatment of air samples, the first results on the integration of PC filters were encouraging. Nevertheless, system modifications are needed to better adapt the Midass system for the monitoring of the microbiological water quality.

Detection of single nucleotide polymorphisms by minisequencing on a polypyrrole DNA chip designed for medical diagnosis.

With the increasing availability of genetic information and its relationship to human diseases, there is a growing need in the medical diagnostic field for technologies that can proceed to the parallel genotyping of multiple markers. In this paper, we report the development of a new flexible microarray-based method that aims to be inexpensive, accurate, and adapted to routine analysis. The construction of the MICAM (MICrosystem for Analysis in Medicine) DNA chip is based on the controlled electro-synthesis of a conducting polymer film bearing oligonucleotide probes on gold electrodes. First, accessible 3'OH-ends of grafted probes are directly used to conduct single template-dependent nucleotide extension reactions with fluorescence-labeled chain terminators. Then, the fluorescence of incorporated dideoxynucleotides on controls and probes of interest are recorded to assess base calling. Here, we present the development of the methodology to assign the genotype of TP53 (tumor protein p53) codon 72 polymorphism and its application to analysis of genomic DNA from cell lines and from human colorectal samples. The genotyping results obtained by mini-sequencing on the polypyrrole DNA chip were 100% concordant with data obtained by polymerase chain reaction-restriction fragment length polymorphism and direct sequencing. Moreover, the developed probe array assay has been successfully applied to the detection of TP53 loss of heterozygosity.

Suppression of Escherichia coli formate hydrogenlyase activity by trimethylamine N-oxide is due to drainage of the inducer formate.

The effect of the addition of trimethylamine N-oxide (TMAO) in the growth medium on Escherichia coli anaerobic fermentative and respiratory pathways was examined. Formate dehydrogenase H (FDH-H) activity was totally repressed by the addition of 40 mM TMAO, whereas the overall hydrogenase (HYD) activity was reduced by 25%. Accordingly, expression of lacZ operon fusions with the fdhF and hycB structural genes specifying FDH-H and HYD3 was reduced sevenfold and eightfold, respectively, leading to suppression of an active formate hydrogenlyase system. In contrast, global respiratory formate-dependent phenazine methosulphate reductase (FDH-PMS) activity, which consists of both the major anaerobic FDH-N enzyme and the aerobic FDH-Z isoenzyme, was increased approximately twofold. This was corroborated by a 2.5-fold stimulation of the sole fdoG-uidA transcriptional fusion which reflects the synthesis of the respiratory aerobic FDH-Z enzyme. In fdhD, fdhE or torA mutants lacking either FDH-PMS activity or TMAO reductase (TOR) activity, the formate hydrogenlyase pathway was no longer inhibited by TMAO. In addition, introduction of 30 mM formate in the growth medium was found to relieve the repressive effect of TMAO in the wild-type strain. When TMAO was added as terminal electron acceptor a significant enhancement of anaerobic growth was observed with the wild-type strain and the fdoG mutant. It was associated with the concomitant suppression of the formate hydrogenlyase enzymes. This was in contrast to the fdnG and torA mutants whose growth pattern and fermentative enzymes remained unaffected. Taken together, these results strongly suggest that formate-dependent reduction of TMAO via FDH-N and TOR reduces the amount of formate available for induction of the formate hydrogenlyase pathway.