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International audience; Interest has been rekindled in the old antibiotic fosfomycin, partly because of its ability to penetrate biofilm. Using a transcriptomic approach, we investigated the modifications induced by fosfomycin in sessile cells of a clinical Staphylococcus aureus isolated from a device-associated infection. Cells still able to form biofilm after 4 h of incubation in the presence of subinhibitory concentrations of fosfomycin and cells from 24-h-old biofilm later submitted to fosfomycin had 6.77% and 9.41%, respectively, of differentially expressed genes compared with their antibiotic-free control. Fosfomycin induced mostly downregulation of genes assigned to nucleotide, amino acid and carbohydrate transport, and metabolism. Adhesins and capsular biosynthesis proteins encoding genes were downregulated in fosfomycin-grown biofilm, whereas the murein hydrolase regulator lgrA and a D-lactate dehydrogenase-encoding gene were upregulated. In fosfomycin-treated biofilm, the expression of genes encoding adhesins, the cell wall biosynthesis protein ScdA, and to a lesser extent the fosfomycin target MurA was also decreased. Unattached cells surrounding fosfomycin-grown biofilm showed greater ability to form aggregates than their counterparts obtained without fosfomycin. Reducing their global metabolism and lowering cell wall turnover would allow some S. aureus cells to grow in biofilm despite fosfomycin stress while promoting hyperadherent phenotype in the vicinity of the fosfomycin-treated biofilm.

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.

Introduction. The worldwide emergence of carbapenem resistance in Gram-negative bacteria makes the development of simple tests mandatory to identify antimicrobial resistance mechanisms. Enzymatic and membrane barriers are the prominent resistance mechanisms described in these bacteria. Several tests are currently used to detect carbapenemase activities. Aim. However, a simple test for the identification of membrane-associated mechanisms of resistance is not yet available and this mechanism is often inferred after the exclusion of a carbapenemase in carbapenem-resistant Gram-negative bacteria. Methodology. Different media (liquid and solid) containing a membrane permeabilizer were tested to identify the existence of a membrane barrier. Here, polymyxin B nonapeptide (PMBN) was selected to bypass the role of impermeability in clinical carbapenem-resistant Enterobacteriaceae , including Escherichia coli , Enterobacter cloacae , Klebsiella pneumoniae and Klebsiella aerogenes isolates. In parallel, the expression of porins (OmpC and OmpF types) was checked in the various bacterial strains in order to search for a correlation between the restoration of susceptibility and the expression of porin. Results. Using a large number of clinical isolates, PMBN associated with a carbapenem allowed us to detect porin-deficient isolates with a sensitivity ranging from 89 to 93 % and a specificity ranging from 86 to 100 %. Conclusion. This paves the way for a diagnostic assay allowing the detection of this membrane-associated mechanism of resistance in Enterobacteriaceae .

The evolutionary success of bacteria depends greatly on their capacity to continually generate phenotypic diversity. Structured environments are particularly favorable for diversification because of attenuated clonal interference, which renders selective sweeps nearly impossible and enhances opportunities for adaptive radiation. We examined at the microscale level the emergence and the spatial and temporal dynamics of phenotypic diversity and their underlying causes in Escherichia coli colonies. An important dynamic heterogeneity in the growth, metabolic activity, morphology, gene expression patterns, stress response induction, and death patterns among cells within colonies was observed. Genetic analysis indicated that the phenotypic variation resulted mostly from mutations and that indole production, oxidative stress, and the RpoS-regulated general stress response played an important role in the generation of diversity. We observed the emergence and persistence of phenotypic variants within single colonies that exhibited variable fitness compared to the parental strain. Some variants showed improved capacity to produce biofilms, whereas others were able to use different nutrients or to tolerate antibiotics or oxidative stress. Taken together, our data show that bacterial colonies provide an ecological opportunity for the generation and maintenance of vast phenotypic diversity, which may increase the probability of population survival in unpredictable environments.

The Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) can form under oxidizing conditions a supramolecular complex with the regulatory protein CP12. Both GAPDH and PRK activities are inhibited within the complex, but they can be fully restored by reduced thioredoxins (TRXs). We have investigated the interactions of eight different chloroplast thioredoxin isoforms (TRX f1, m1, m2, m3, m4, y1, y2, x) with GAPDH (A 4 , B 4 , and B 8 isoforms), PRK and CP12 (isoform 2), all from Arabidopsis thaliana . In the complex, both A 4 -GAPDH and PRK were promptly activated by TRX f1, or more slowly by TRXs m1 and m2, but all other TRXs were ineffective. Free PRK was regulated by TRX f1, m1, or m2, while B 4 - and B 8 -GAPDH were absolutely specific for TRX f1. Interestingly, reductive activation of PRK caged in the complex was much faster than reductive activation of free oxidized PRK, and activation of A 4 -GAPDH in the complex was much faster (and less demanding in terms of reducing potential) than activation of free oxidized B 4 - or B 8 -GAPDH. It is proposed that CP12-assembled supramolecular complex may represent a reservoir of inhibited enzymes ready to be released in fully active conformation following reduction and dissociation of the complex by TRXs upon the shift from dark to low light. On the contrary, autonomous redox-modulation of GAPDH (B-containing isoforms) would be more suited to conditions of very active photosynthesis.

Here, we report the genome sequence of Staphylococcus aureus LYO-S2, an isolate with sequence type (ST) 45 that was isolated in 2001 from a prosthetic joint infection.

International audience; Treatment of orthopaedic infections remains challenging owing to the inability of antibiotics to eradicate biofilms and prevent their regrowth. The present study characterized the effects of 12 antibiotics on in vitro biofilm formed by a representative strain of meticillin-susceptible Staphylococcus aureus (MSSA) isolated from a bone infection. Determination of the minimum biofilm eradication concentrations indicated that in vitro eradication of 24 h-old biofilms required concentrations up to 51,200 times higher than MICs. The influence of the same panel of antibiotics was also investigated on biofilm formation at concentrations including the breakpoints, by numbering viable cells in the suspensions (individual cells) and the biofilm biomass. Except for fusidic acid, the presence of antibiotics during the initial steps of biofilm formation resulted in significant decreases in the number of sessile viable bacteria at the highest concentrations tested. Ceftarolin, daptomycin, fosfomycin, gentamicin, ofloxacin, rifampicin and vancomycin were the most effective drugs. Confocal microscopy analysis indicated that daptomycin was more efficient at bacteria lysis than gentamicin and vancomycin. However, viable individual cells were still detectable in the assays performed with ceftarolin, fosfomycin, ofloxacin, rifampicin and vancomycin at concentrations for which no sessile cells were detected. Although none of the molecules tested was effective at classical therapeutic concentrations against 24 h-old MSSA biofilms, all except fusidic acid were able to impair biofilm formation at concentrations near the breakpoints. However, presence of viable individual unattached cells could imply a significant risk of microbial dissemination and increased risk of infections.

Thioredoxin f (TRXf) is a key factor in the redox regulation of chloroplastic carbon fixation enzymes, whereas glutathione is an important thiol buffer whose status is modulated by stress conditions. Here, we report specific glutathionylation of TRXf. A conserved cysteine is present in the TRXf primary sequence, in addition to its two active-site cysteines. The additional cysteine becomes glutathionylated when TRXf is exposed to oxidized glutathione or to reduced glutathione plus oxidants. No other chloroplastic TRX, from either Arabidopsis or Chlamydomonas , is glutathionylated under these conditions. Glutathionylation decreases the ability of TRXf to be reduced by ferredoxin-thioredoxin reductase and results in impaired light activation of target enzymes in a reconstituted thylakoid system. Although several mammalian proteins undergoing glutathionylation have already been identified, TRXf is among the first plant proteins found to undergo this posttranslational modification. This report suggests that a crosstalk between the TRX and glutathione systems mediates a previously uncharacterized form of redox signaling in plants in stress conditions.

The sequencing of the genome of Arabidopsis thaliana revealed that this plant contained numerous isoforms of thioredoxin (Trx), a protein involved in thiol-disulfide exchanges. On the basis of sequence comparison, seven putative chloroplastic Trxs have been identified, four belonging to the m-type, two belonging to the f-type, and one belonging to a new x-type. In the present work, these isoforms were produced and purified as recombinant proteins without their putative transit peptides. Their activities were tested with two known chloroplast thioredoxin targets: NADP-malate dehydrogenase and fructose-1,6-bisphosphatase and also with a chloroplastic 2-Cys peroxiredoxin. The study confirms the strict specificity of fructose-bisphosphatase for Trx f, reveals that some Trxs are unable to activate NADP-malate dehydrogenase, and shows that the new x-type is the most efficient substrate for peroxiredoxin while being inactive toward the two other targets. This suggests that this isoform might be specifically involved in resistance against oxidative stress. Three-dimensional modeling shows that one of the m-type Trxs, Trx m3, which has no activity with any of the three targets, exhibits a negatively charged surface surrounding the active site. A green fluorescent protein approach confirms the plastidial localization of these Trxs.

The completion of the sequencing of the Arabidopsis genome revealed the multiplicity of plant thioredoxins, dithiol proteins involved in redox regulation, due to their ability to undergo thiol-disulfide interchanges with numerous proteins. An examination of the expressed sequence tag (EST) databanks of the unicellular green alga Chlamydomonas reinhardtii reveals also multiple thioredoxin types, but with fewer isoforms in each type than for higher plants. The pioneering work on the Chlamydomonas thioredoxin systems, mainly based on biochemical approaches, is summarised and the EST databanks analysed from a qualitative (different ESTs) and quantitative (EST abundance) viewpoints. It is proposed that Chlamydomonas can be a suitable organism to uncover basic functions of each thioredoxin type.

The sequencing of the Arabidopsis genome revealed a multiplicity of thioredoxins (TRX), ubiquitous protein disulfide oxido-reductases. We have analyzed the TRX family in the genome of the unicellular green alga Chlamydomonas reinhardtii and identified eight different thioredoxins for which we have cloned and sequenced the corresponding cDNAs. One of these TRXs represents a new type that we named TRX y. This most probably chloroplastic TRX is highly conserved in photosynthetic organisms. The biochemical characterization of the recombinant protein shows that it exhibits a thermal stability profile and specificity toward target enzymes completely different from those of TRXs characterized so far.

A pesar de que el interes por el estudio del discurso del turismo en lengua francesa parece haber perdido protagonismo en los ultimos anos, destacamos un interes creciente por los articulos de prensa. Este genero adquiere relevancia por su alta frecuencia en la prensa actual, ademas de ofrecer una mayor libertad a la hora de ser redactados. Esta flexibilidad les convierte en textos de una menor rigidez, lo que ha contribuido a que algunos investigadores hablen de un alto grado de hibridacion generica. Sin embargo, pudimos advertir que en esos estudios el aspecto promocional del reportaje no quedaba reflejado en absoluto. Por tanto, este trabajo pretende poner de manifiesto otros aspectos muy relevantes del articulo de prensa referente a un destino turistico, que se desmarca del resto de los textos turisticos que son fundamentalmente elogiosos y euforizantes. El articulo de prensa, como hemos pretendido demostrar, no se puede considerar como un texto prescriptivo sino como un elemento escrito que participa en la promocion de una imagen, en nuestro caso de un destino turistico. Para desarrollar este estudio hemos recopilado un corpus de articulos pertenecientes al archivo de Turespana, denominados “reportajes” por los profesionales, delimitado al periodo 2002-2008, publicados por la prensa extranjera de diferentes paises de lengua francesa, sobre las ciudades espanolas que poseen el distintivo de Patrimonio de la Humanidad, consideradas como destino turistico de tipo cultural urbano. Son reportajes obtenidos tras la realizacion de un fam trips o press trips, que consiste en la invitacion por parte de los gestores de turismo a diferentes periodistas procedentes de los paises que mas tarde publicaran estos articulos. Con este corpus pretendimos dejar patente el papel promocional del reportaje, partiendo de la funcion de los recursos turisticos desde el punto de vista del enfoque del marketing turistico. Para ello elaboramos una “grille” a partir de los recursos turisticos que previamente seleccionamos en funcion del tipo de turismo tratado. Con este metodo analizamos los recursos de cada ciudad con el fin de establecer un mismo criterio para todas, de manera sintetica, ademas de contemplar lo que decidimos llamar recursos expresivos, para poder analizar el texto en todos sus aspectos. Las conclusiones sobre la lengua del turismo no pueden ser significativas si no entendemos que la mayoria de los textos estan realizados con el exclusivo fin de promocionar o vender un destino. El discurso puede ser diferente segun el segmento de turistas a quien va dirigido, lo que implica que el redactor se adaptara a esas circunstancias, y al final, cualquier reportaje depende tambien del estilo en la redaccion del periodista. De ahi la impresion de unos textos llamados “hibridos”, que entendemos que si lo son, pero lo que ha procurado este trabajo es poner de manifiesto las razones objetivas de dicha impresion.

The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the lca (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classification platforms used. The remaining isolates were mostly identified correctly at the genus level due to the limited resolution of 16S rDNA sequencing. Discrepancies between both 16S rDNA platforms were due to differences in database content and the algorithm used, and could amount to up to 10.5 %. Up to 1.4 % of the analyses were found to be inconclusive. It is important to realize that despite the overall good performance of the pipelines for analysis, some inconclusive results remain that require additional in-depth analysis performed using supplementary methods.

Arabidopsis (Arabidopsis thaliana) plants were grown in a hydroponic culture system for 7 to 14 d in the absence or presence of 75 microM Cd or 75 microM Cu. The Cu treatment resulted in visual leaf symptoms, together with anthocyanin accumulation and loss of turgor. Pronounced lipid peroxidation, which was detected by autoluminescence imaging and malondialdehyde titration, was observed in Cu-treated leaves. The Cd treatment also resulted in loss of leaf pigments but lipid peroxidation and oxidative stress were less pronounced than in the leaves exposed to Cu. Analysis of low-molecular-weight chloroplast and cytosolic antioxidants (ascorbate, glutathione, tocopherols, carotenoids) and antioxidant enzymes (thiol-based reductases and peroxidases) revealed relatively few responses to metal exposure. However, there was a marked increase in vitamin E (alpha-tocopherol) in response to Cd and Cu treatments. Ascorbate increased significantly in Cu-exposed leaves. Other antioxidants either remained stable or decreased in response to metal stress. Transcripts encoding enzymes of the vitamin E biosynthetic pathway were increased in response to metal exposure. In particular, VTE2 mRNA was enhanced in Cu- and Cd-treated plants, while VTE5 and hydroxylpyruvate dioxygenase (HPPD) mRNAs were only up-regulated in Cd-treated plants. Consistent increases in HPPD transcripts and protein were observed. The vitamin E-deficient (vte1) mutant exhibited an enhanced sensitivity towards both metals relative to the wild-type (WT) control. Unlike the vte1 mutants, which showed enhanced lipid peroxidation and oxidative stress in the presence of Cu or Cd, the ascorbate-deficient (vtc2) mutant showed WT responses to metal exposure. Taken together, these results demonstrate that vitamin E plays a crucial role in the tolerance of Arabidopsis to oxidative stress induced by heavy metals such as Cu and Cd.

We provide here an exhaustive overview of the glutathione (GSH) peroxidase (Gpx) family of poplar (Populus trichocarpa). Although these proteins were initially defined as GSH dependent, in fact they use only reduced thioredoxin (Trx) for their regeneration and do not react with GSH or glutaredoxin, constituting a fifth class of peroxiredoxins. The two chloroplastic Gpxs display a marked selectivity toward their electron donors, being exclusively specific for Trxs of the y type for their reduction. In contrast, poplar Gpxs are much less specific with regard to their electron-accepting substrates, reducing hydrogen peroxide and more complex hydroperoxides equally well. Site-directed mutagenesis indicates that the catalytic mechanism and the Trx-mediated recycling process involve only two (cysteine [Cys]-107 and Cys-155) of the three conserved Cys, which form a disulfide bridge with an oxidation-redox midpoint potential of −295 mV. The reduction/formation of this disulfide is detected both by a shift on sodium dodecyl sulfate-polyacrylamide gel electrophoresis or by measuring the intrinsic tryptophan fluorescence of the protein. The six genes identified coding for Gpxs are expressed in various poplar organs, and two of them are localized in the chloroplast, with one colocalizing in mitochondria, suggesting a broad distribution of Gpxs in plant cells. The abundance of some Gpxs is modified in plants subjected to environmental constraints, generally increasing during fungal infection, water deficit, and metal stress, and decreasing during photooxidative stress, showing that Gpx proteins are involved in the response to both biotic and abiotic stress conditions.

Peroxiredoxin Q (Prx Q) is one out of 10 peroxiredoxins encoded in the genome of Arabidopsis thaliana, and one out of four that are targeted to plastids. Peroxiredoxin Q functions as a monomeric protein and represents about 0.3% of chloroplast proteins. It attaches to the thylakoid membrane and is detected in preparations enriched in photosystem II complexes. Peroxiredoxin Q decomposes peroxides using thioredoxin as an electron donor with a substrate preference of H(2)O(2) > cumene hydroperoxide >> butyl hydroperoxide >> linoleoyl hydroperoxide and insignificant affinity towards complex phospholipid hydroperoxide. Plants with decreased levels of Prx Q did not have an apparently different phenotype from wildtype at the plant level. However, similar to antisense 2-cysteine (2-Cys) Prx plants [Baier, M. et al. (2000)Plant Physiol., 124, 823-832], Prx Q-deficient plants had a decreased sensitivity to oxidants in a leaf slice test as indicated by chlorophyll a fluorescence measurements. Increased fluorescence ratios of photosystem II to I at 77 K and modified transcript levels of plastid- and nuclear-encoded proteins show that regulatory mechanisms are at work to compensate for the lack of Prx Q. Apparently Prx Q attaches to photosystem II and has a specific function distinct from 2-Cys peroxiredoxin in protecting photosynthesis. Its absence causes metabolic changes that are sensed and trigger appropriate compensatory responses.

The ferredoxin/thioredoxin reductase (FTR) is the key enzyme of a light dependent redox regulatory system controlling enzyme activities in oxygenic photosynthetic cells. It is composed of two dissimilar subunits. The catalytic subunit contains a [4Fe-4S] cluster and a redox-active disulfide bridge as the active site. The function of the second subunit, named the variable subunit because it has less conserved primary sequence and length, is not yet known. In order to get insights into the physiological role and importance of FTR, we studied two Arabidopsis mutant lines in which one of two genes encoding FTRA subunit was disrupted by T-DNA insertion. In FTRA1 mutants, the absence of the corresponding transcript was not compensated by the increase in the level of FTRA2 mRNA. Mutant plants exhibited phenotypic perturbations when compared with wild-type plants. Disruptants were found significantly more sensitive to oxidative stress as imposed under high light or in the presence of paraquat. Mutants were further characterized at the biochemical level. Despite the fact that no difference was found by immunodetection of FTR polypeptides, evidence for an impaired FTR system occurring in the mutants was obtained by measuring the endogenous activation rate of one of its targets. In the leaves of mutants placed under normal culture conditions, NADP-dependent malate dehydrogenase (NADP-MDH) activation rate was abnormally low. A partially compensating increase of the enzyme activity was found as well as a higher amount of 2-cys-peroxiredoxin. Our results provide in planta confirmation of the antioxidant role previously proposed for some of the plastidial thioredoxins from Arabidopsis thaliana. The variable subunit of the FTR proved to be important, but its precise role remains to be established.

The plant plastidial thioredoxins (Trx) are involved in the light-dependent regulation of many enzymatic activities, owing to their thiol-disulfide interchange activity. Three different types of plastidial Trx have been identified and characterized so far: the m-, f-, and x-types. Recently, a new putative plastidial type, the y-type, was found. In this work the two isoforms of Trx y encoded by the nuclear genome of Arabidopsis (Arabidopsis thaliana) were characterized. The plastidial targeting of Trx y has been established by the expression of a Trx∷GFP fusion protein. Then both isoforms were produced as recombinant proteins in their putative mature forms and purified to characterize them by a biochemical approach. Their ability to activate two plastidial light-regulated enzymes, NADP-malate dehydrogenase (NADP-MDH) and fructose-1,6-bisphosphatase, was tested. Both Trx y were poor activators of fructose-1,6-bisphosphatase and NADP-MDH; however, a detailed study of the activation of NADP-MDH using site-directed mutants of its regulatory cysteines suggested that Trx y was able to reduce the less negative regulatory disulfide but not the more negative regulatory disulfide. This property probably results from the fact that Trx y has a less negative redox midpoint potential (−337 mV at pH 7.9) than thioredoxins f and m. The y-type Trxs were also the best substrate for the plastidial peroxiredoxin Q. Gene expression analysis showed that Trx y2 was mainly expressed in leaves and induced by light, whereas Trx y1 was mainly expressed in nonphotosynthetic organs, especially in seeds at a stage of major accumulation of storage lipids.