Naringenin Inhibition of the Pseudomonas aeruginosa Quorum Sensing Response Is Based on Its Time-Dependent Competition With N-(3-Oxo-dodecanoyl)-L-homoserine Lactone for LasR Binding

Bacterial quorum sensing (QS) is a cell-to-cell communication system that governs the expression of a large set of genes involved in bacterial-host interactions, including the production of virulence factors. Conversely, the hosts can produce anti-QS compounds to impair virulence of bacterial pathogens. One of these inhibitors is the plant flavonoid naringenin, which impairs the production of QS-regulated Pseudomonas aeruginosa virulence factors. In the present work, we analyze the molecular basis for such inhibition. Our data indicate that naringenin produces its effect by directly binding the QS regulator LasR, hence competing with its physiological activator, N-(3-oxo-dodecanoyl)-L-homoserine lactone (3OC12-HSL). The in vitro analysis of LasR binding to its cognate target DNA showed that the capacity of naringenin to outcompete 3OC12-HSL, when the latter is previously bound to LasR, is low. By using an E. coli LasR-based biosensor strain, which does not produce 3OC12-HSL, we determined that the inhibition of LasR is more efficient when naringenin binds to nascent LasR than when this regulator is already activated through 3OC12-HSL binding. According to these findings, at early exponential growth phase, when the amount of 3OC12-HSL is low, naringenin should proficiently inhibit the P. aeruginosa QS response, whereas at later stages of growth, once 3OC12-HSL concentration reaches a threshold enough for binding LasR, naringenin would not efficiently inhibit the QS response. To test this hypothesis, we analyze the potential effect of naringenin over the QS response by adding naringenin to P. aeruginosa cultures at either time zero (early inhibition) or at stationary growth phase (late inhibition). In early inhibitory conditions, naringenin inhibited the expression of QS-regulated genes, as well as the production of the QS-regulated virulence factors, pyocyanin and elastase. Nevertheless, in late inhibitory conditions, the P. aeruginosa QS response was not inhibited by naringenin. Therefore, this time-dependent inhibition may compromise the efficiency of this flavonoid, which will be effective just when used against bacterial populations presenting low cellular densities, and highlight the importance of searching for QS inhibitors whose mechanism of action does not depend on the QS status of the population.

Toxin ζ Reduces the ATP and Modulates the Uridine Diphosphate-N-acetylglucosamine Pool

Toxin ζ expression triggers a reversible state of dormancy, diminishes the pool of purine nucleotides, promotes (p)ppGpp synthesis, phosphorylates a fraction of the peptidoglycan precursor uridine diphosphate-N-acetylglucosamine (UNAG), leading to unreactive UNAG-P, induces persistence in a reduced subpopulation, and sensitizes cells to different antibiotics. Here, we combined computational analyses with biochemical experiments to examine the mechanism of toxin ζ action. Free ζ toxin showed low affinity for UNAG. Toxin ζ bound to UNAG hydrolyzed ATP·Mg2+, with the accumulation of ADP, Pi, and produced low levels of phosphorylated UNAG (UNAG-P). Toxin ζ, which has a large ATP binding pocket, may temporally favor ATP binding in a position that is distant from UNAG, hindering UNAG phosphorylation upon ATP hydrolysis. The residues D67, E116, R158 and R171, involved in the interaction with metal, ATP, and UNAG, were essential for the toxic and ATPase activities of toxin ζ; whereas the E100 and T128 residues were partially dispensable. The results indicate that ζ bound to UNAG reduces the ATP concentration, which indirectly induces a reversible dormant state, and modulates the pool of UNAG.

Modelling the metabolism of protein secretion through the Tat route in Streptomyces lividans

Background

Streptomyces lividans has demonstrated its value as an efficient host for protein production due to its ability to secrete functional proteins directly to the media. Secretory proteins that use the major Sec route need to be properly folded outside the cell, whereas secretory proteins using the Tat route appear outside the cell correctly folded. This feature makes the Tat system very attractive for the production of natural or engineered Tat secretory proteins. S. lividans cells are known to respond differently to overproduction and secretion of Tat versus Sec proteins. Increased understanding of the impact of protein secretion through the Tat route can be obtained by a deeper analysis of the metabolic impact associated with protein production, and its dependence on protein origin, composition, secretion mechanisms, growth phases and nutrients. Flux Balance Analysis of Genome-Scale Metabolic Network models provides a theoretical framework to investigate cell metabolism under different constraints.

Results

We have built new models for various S. lividans strains to better understand the mechanisms associated with overproduction of proteins secreted through the Tat route. We compare models of an S. lividans Tat-dependent agarase overproducing strain with those of the S. lividans wild-type, an S. lividans strain carrying the multi-copy plasmid vector and an α-amylase Sec-dependent overproducing strain. Using updated genomic, transcriptomic and experimental data we could extend existing S. lividans models and produce a new model which produces improved results largely extending the coverage of S. lividans strains, the number of genes and reactions being considered, the predictive behaviour and the dependence on specification of exchange constraints. Comparison of the optimized solutions obtained highlights numerous changes between Tat- and Sec-dependent protein secreting strains affecting the metabolism of carbon, amino acids, nucleotides, lipids and cofactors, and variability analysis predicts a large potential for protein overproduction.

Conclusions

This work provides a detailed look to metabolic changes associated to Tat-dependent protein secretion reproducing experimental observations and identifying changes that are specific to each secretory route, presenting a novel, improved, more accurate and strain-independent model of S. lividans, thus opening the way for enhanced metabolic engineering of protein overproduction in S. lividans.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1199-3) contains supplementary material, which is available to authorized users.

Looking for Rhizobacterial Ecological Indicators in Agricultural Soils Using 16S rRNA metagenomic Amplicon Data

INTRODUCTION

Biological communities present in soil are essential to sustainable and productive agricultural practices; however, an accurate determination of the ecological status of agricultural soils remains to date an elusive task. An ideal indicator should be pervasive, play a relevant role in the ecosystem, show a rapid and proportional answer to external perturbations and be easily and economically measurable. Rhizobacteria play a major role in determining soil properties, becoming an attractive candidate for the detection of ecological indicators. The application of massive sequencing technologies to metagenomic analysis is providing an increasingly more precise view of the structure and composition of soil communities. In this work, we analyse soil rhizobacterial composition under various stress levels to search for potential ecological indicators.

GENERAL BIODIVERSITY INDICATORS

Our results suggest that the Shannon index requires observation of a relatively large number of individuals to be representative of the true population diversity, and that the Simpson index may underestimate rare taxa in rhizobacterial environments.

TAXONOMICAL CLASSIFICATION METHODS

Detection of indicator taxa requires comparison of taxonomical classification of sequences. We have compared RDP classifier, RTAX and similarity-based taxonomical classification and selected the latter for taxonomical assignment because it provides larger detail.

TAXONOMY-BASED ECOLOGICAL INDICATORS

The study of significant variations in common, clearly identified, taxa, using paired datasets allows minimization of non-treatment effects and avoidance of false positives. We have identified taxa associated to specific perturbations as well as taxa generally affected in treated soils. Changes in these taxa, or combinations of them, may be used as ecological indicators of soil health. The overall number and magnitude of changes detected in taxonomic groups does also increase with stress. These changes constitute an alternative indicator to measuring specific taxa, although their determination requires large sample sizes, better obtained by massive sequencing.

SUMMARY

The main ecological indicators available are the Shannon index, OTU counts and estimators, overall detection of the number and proportion of changes, and changes of specific indicator taxa. Massive sequencing remains the most accurate tool to measure rhizobacterial ecological indicators. When massive sequencing is not an option, various cultivable taxonomic groups, such as specific groups in the Actinobacteria tree, are attractive as potential indicators of large disruptions to the rhizobiome.

Effect of herbicide combinations on Bt-maize rhizobacterial diversity

Reports of herbicide resistance events are proliferating worldwide, leading to new cultivation strategies using combinations of pre-emergence and post-emergence herbicides. We analyzed the impact during a one-year cultivation cycle of several herbicide combinations on the rhizobacterial community of glyphosate-tolerant Bt-maize and compared them to those of the untreated or glyphosate-treated soils. Samples were analyzed using pyrosequencing of the V6 hypervariable region of the 16S rRNA gene. The sequences obtained were subjected to taxonomic, taxonomy-independent, and phylogeny-based diversity studies, followed by a statistical analysis using principal components analysis and hierarchical clustering with jackknife statistical validation. The resilience of the microbial communities was analyzed by comparing their relative composition at the end of the cultivation cycle. The bacterial communites from soil subjected to a combined treatment with mesotrione plus s-metolachlor followed by glyphosate were not statistically different from those treated with glyphosate or the untreated ones. The use of acetochlor plus terbuthylazine followed by glyphosate, and the use of aclonifen plus isoxaflutole followed by mesotrione clearly affected the resilience of their corresponding bacterial communities. The treatment with pethoxamid followed by glyphosate resulted in an intermediate effect. The use of glyphosate alone seems to be the less aggressive one for bacterial communities. Should a combined treatment be needed, the combination of mesotrione and s-metolachlor shows the next best final resilience. Our results show the relevance of comparative rhizobacterial community studies when novel combined herbicide treatments are deemed necessary to control weed growth..

Analysis of metagenomic data containing high biodiversity levels

In this paper we have addressed the problem of analysing Next Generation Sequencing samples with an expected large biodiversity content. We analysed several well-known 16S rRNA datasets from experimental samples, including both large and short sequences, in numbers of tens of thousands, in addition to carefully crafted synthetic datasets containing more than 7000 OTUs. From this data analysis several patterns were identified and used to develop new guidelines for experimentation in conditions of high biodiversity. We analysed the suitability of different clustering packages for these type of situations, the problem of even sampling, the relative effectiveness of Chao1 and ACE estimators as well as their effect on sampling size for a variety of population distributions. As regards practical analysis procedures, we advocated an approach that retains as much high-quality experimental data as possible. By carefully applying selection rules combining the taxonomic assignment with clustering strategies, we derived a set of recommendations for ultra-sequencing data analysis at high biodiversity levels.

Effect of Cry1Ab protein on rhizobacterial communities of Bt-maize over a four-year cultivation period

Background

Bt-maize is a transgenic variety of maize expressing the Cry toxin from Bacillus turingiensis. The potential accumulation of the relative effect of the transgenic modification and the cry toxin on the rhizobacterial communities of Bt-maize has been monitored over a period of four years.

Methodology/Principal Findings

The accumulative effects of the cultivation of this transgenic plant have been monitored by means of high throughput DNA pyrosequencing of the bacterial DNA coding for the 16S rRNA hypervariable V6 region from rhizobacterial communities. The obtained sequences were subjected to taxonomic, phylogenetic and taxonomic-independent diversity studies. The results obtained were consistent, indicating that variations detected in the rhizobacterial community structure were possibly due to climatic factors rather than to the presence of the Bt-gene. No variations were observed in the diversity estimates between non-Bt and Bt-maize.

Conclusions/Significance

The cultivation of Bt-maize during the four-year period did not change the maize rhizobacterial communities when compared to those of the non-Bt maize. This is the first study to be conducted with Bt-maize during such a long cultivation period and the first evaluation of rhizobacterial communities to be performed in this transgenic plant using Next Generation Sequencing.

Effect of the herbicide glyphosate on the culturable fraction of glyphosate-tolerant maize rhizobacterial communities using two different growth media

A comparison was drawn between the effect of glyphosate (Roundup Plus), a post-emergence applied herbicide, and Harness GTZ, a pre-emergence applied herbicide, on the culturable fraction of the rhizobacterial communities of genetically modified NK603 glyphosate-tolerant maize. Two different non-selective rich media were used to grow fast-growing culturable bacteria, BHI and NB, as a more accurate estimation of the soil fast-growing culturable bacterial population would be obtained from the results of cultivating in more than one medium. The potential effect was monitored by direct amplification, cloning and sequencing of bacterial DNA encoding 16S rRNA, and high-throughput DNA pyrosequencing of the bacterial DNA coding for the 16S rRNA hypervariable V6 region from bacterial communities grown in the two different media. The estimated relative composition of the culturable maize rhizobacterial population varied considerably in accordance with the growth medium used. Both herbicides do, in fact, affect the maize rhizobacterial communities, glyphosate being, to a great extent, the less aggressive herbicide, regardless of the cultivation medium used. The pyrosequencing analysis of the fast-growing bacterial populations from the different soils represents a useful and invaluable tool to estimate the bacterial biodiversity of the culturable rhizobacteria of agricultural soils.

RB1 gene mutation up-date, a meta-analysis based on 932 reported mutations available in a searchable database

Background

Retinoblastoma, a prototype of hereditary cancer, is the most common intraocular tumour in children and potential cause of blindness from therapeutic eye ablation, second tumours in germ line carrier's survivors, and even death when left untreated. The molecular scanning of RB1 in search of germ line mutations lead to the publication of more than 900 mutations whose knowledge is important for genetic counselling and the characterization of phenotypic-genotypic relationships.

Results

A searchable database (RBGMdb) has been constructed with 932 published RB1 mutations. The spectrum of these mutations has been analyzed with the following results: 1) the retinoblastoma protein is frequently inactivated by deletions and nonsense mutations while missense mutations are the main inactivating event in most genetic diseases. 2) Near 40% of RB1 gene mutations are recurrent and gather in sixteen hot points, including twelve nonsense, two missense and three splicing mutations. The remainder mutations are scattered along RB1, being most frequent in exons 9, 10, 14, 17, 18, 20, and 23. 3) The analysis of RB1 mutations by country of origin of the patients identifies two groups in which the incidence of nonsense and splicing mutations show differences extremely significant, and suggest the involvement of predisposing ethnic backgrounds. 4) A significant association between late age at diagnosis and splicing mutations in bilateral retinoblastoma patients suggests the occurrence of a delayed-onset genotype. 5) Most of the reported mutations in low-penetrance families fall in three groups: a) Mutations in regulatory sequences at the promoter resulting in low expression of a normal Rb; b) Missense and in-frame deletions affecting non-essential sequence motifs which result in a partial inactivation of Rb functions; c) Splicing mutations leading to the reduction of normal mRNA splicing or to alternative splicing involving either true oncogenic or defective (weak) alleles.

Conclusion

The analysis of RB1 gene mutations logged in the RBGMdb has shown relevant phenotype-genotype relationships and provided working hypothesis to ascertain mechanisms linking certain mutations to ethnicity, delayed onset of the disease and low-penetrance. Gene profiling of tumors will help to clarify the genetic background linked to ethnicity and variable expressivity or delayed onset phenotypes.

Alterations to complex viscoelasticity of erythrocytes during storage

Rheological alterations produced during the storage of human erythrocytes were studied by means of in vitro viscoelastic parameters. Weekly aliquots of packed red blood cells (PRBC) and whole blood (WB) stored in CPD-adenine were studied for 35 days. Samples were analyzed in Erythrodeformeter both in stationary and oscillating regime. We found that erythrocyte deformability index and all complex viscoelastic parameters are modified by storage. Plasma viscosity and blood viscosity were measured in a cone/plate Viscometer. Blood viscosity at high shear rates shows variations related to conservation time, which are in correlation with the variations observed in the erythrocyte deformability index. Blood viscosity at low shear rate decreases during storage. Rheological tests would demonstrate some alterations in the structural properties of erythrocyte stored as PRBC. These alterations are less than those found in WB. We conclude that plasmatic proteins play a predominant role in the alteration of rheological behavior of erythrocytes during their storage. Consequently, it is important to evaluate not only cellular components but also plasma.

Evaluation of the energy of red blood cell agglutination by monoclonal antibodies

The knowledge of the energy involved in cell-cell interactions has significant implications in biological and medical sciences. Red blood cells (RBC) become mutually adhered when specific (agglutinins) or nonspecific macromolecules bind adjacent cells in an irreversible or reversible form. Flow chamber technique with digital image processing was successfully applied to determine the partial separation, by shear stress, of two RBC agglutinated face to face (doublet) by specific monoclonal antibodies (MAb) and also to evaluate the shear stress required to attain this separation. The work done in separating adhered cells is then easily calculated and serves to evaluate the antibody affinity. In this work, this technique was applied to evaluate the affinity of a monoclonal antibody specific to the blood group A antigen. The specific disaggregation energy gamma (i.e., the work done by the shear stress) required to disrupt a unit of adhered membrane areas between agglutinated cells was calculated. On play back of the image analysis, measurements were taken to determine the force applied to the doublet and the relative separation between both RBC. Values of gamma(d) (from 2.70 to 4.61 x 10(-9) N/cm) were found to be proportional to the density (D = 27 to 55 molecules/microm(2)) of MAb molecules bound on the RBC membrane.

Rheologic characterization of vegetal lectins by dissociation of induced erythrocyte agglutinates

Energy evolved from hemagglutination reaction or spent in dissociating erythrocyte agglutinates has been proved to be an excellent parameter for analyzing cell-cell interactions mediated by bridging molecules such as antibodies or lectins. We developed a new rheo-optical method to estimate the energy of dissociation of red blood cell agglutinates. In a Couette shear field agglutinates can be dissociated until a suspension of monodispersed cells is obtained. Intensity of light backscattered by suspended agglutinates increases during their mechanical dissociation. Variation of backscattered light intensity correlates with the energy spent in the process. The adhesive energy of erythrocyte agglutination induced by lectins has been estimated by applying this method. Two specific lectins (Dolichus Biflorus agglutinin and Ulex Europaeus agglutinin) and a new lectin obtained from Amarantus Cruentus seeds which specificity is unknown were studied. Results obtained in this work for Dolichus Biflorus lectin are comparable with values published by other authors. An asymptotic decrease of adhesive energy was observed when the mechanical dissociation was applied several times on the same sample. Our results suggest that the cell detachment is accompanied by the extraction of membrane receptors. This finding is consistent with results obtained by other authors.

A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria

A search of sequence data bases for a tridecamer transcription termination signal, previously described in human mtDNA as being responsible for the accumulation of mitochondrial ribosomal RNAs (rRNAs) in excess over the rest of mitochondrial genes, has revealed that this termination signal occurs in equivalent positions in a wide variety of organisms from protozoa to mammals. Due to the compact organization of the mtDNA, the tridecamer motif usually appears as part of the 3' adjacent gene sequence. Because in phylogenetically widely separated organisms the mitochondrial genome has experienced many rearrangements, it is interesting that its occurrence near the 3' end of the large rRNA is independent of the adjacent gene. The tridecamer sequence has diverged in phylogenetically widely separated organisms. Nevertheless, a well-conserved heptamer--TGGCAGA, the mitochondrial rRNA termination box--can be defined. Although extending the experimental evidence of its role as a transcription termination signal in humans will be of great interest, its evolutionary conservation strongly suggests that mitochondrial rRNA transcription termination could be a widely conserved mechanism in animals. Furthermore, the conservation of a homologous tridecamer motif in one of the last 3' secondary loops of nonmitochondrial 23S-like rRNAs suggests that the role of the sequence has changed during mitochondrial evolution.

Speciation in the Artemia genus: mitochondrial DNA analysis of bisexual and parthenogenetic brine shrimps

From the cloned mitochondrial DNAs (mtDNAs) isolated from two bisexual species, one Mediterranean, Artemia salina, and one American, Artemia franciscana, and two parthenogenetic (diploid and tetraploid) strains of Artemia parthenogenetica collected in Spain, physical maps have been constructed and compared. They are extremely different among themselves, much more than the differences between Drosophila melanogaster and D. yakuba and in the same range of different mammalian species such as mouse/rat or man/cow. The nucleotide sequences of two regions of mtDNA encoding parts of the cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) genes have been determined in the two bisexual species and the two parthenogenetic strains. Comparisons of these sequences have revealed a high degree of divergence at the nucleotide level, averaging more than 15%, in agreement with the differences found in the physical maps. The majority of the nucleotide changes are silent and there is a strong bias toward transitions, with the C<==>T substitutions being highly predominant. The evolutionary distance between the two Artemia parthenogenetica is high and there is no clear relationship with any of the bisexual species, including the one present nowadays in Spain. Using a combination of molecular (mtDNA) and morphological markers it is possible to conclude that all of these Artemia isolates should be actually considered as belonging to different species, even the two Artemia parthenogenetica diploidica and tetraploidica.

S1 nuclease-sensitive sites in the bithoraxoid region of the Drosophila Ultrabithorax gene

The Ultrabithorax gene is required to specify the third thoracic and first abdominal segments of Drosophila melanogaster. Mutations in the bithoraxoid region, a 40 kb DNA stretch upstream of the Ultrabithorax promoter, affect cis-regulatory elements of the Ultrabithorax gene. We now have identified specific sites in the bithoraxoid region that exhibit S1 nuclease sensitivity in vitro. These sites are not scattered along the DNA but are grouped instead in specific domains. Some of these S1-sensitive sites correlate with known breakpoint or insertional mutations. Others correspond to putative binding sites for transcription factors. The results suggest that unusual secondary structure might be important in chromosomal translocation within regulatory sequences of the Ultrabithorax product or its transcriptional regulation.

Insects as test systems for assessing the potential role of microgravity in biological development and evolution

Gravity and radiation are undoubtedly the two major environmental factors altered in space. Gravity is a weak force, which creates a permanent potential field acting on the mass of biological systems and their cellular components, strongly reduced in space flights. Developmental systems, particularly at very early stages, provide the larger cellular compartments known, where the effects of alterations in the size of the gravity vector on living organisms can be more effectively tested. The insects, one of the more highly evolved classes of animals in which early development occurs in a syncytial embryo, are systems particularly well suited to test these effects and the specific developmental mechanisms affected. Furthermore, they share some basic features such as small size, short life cycles, relatively high radio-resistance, etc. and show a diversity of developmental strategies and tempos advantageous in experiments of this type in space. Drosophila melanogaster, the current biological paradigm to study development, with so much genetic and evolutionary background available, is clearly the reference organism for these studies. The current evidence on the effects of the physical parameters altered in space flights on insect development indicate a surprising correlation between effects seen on the fast developing and relatively small Drosophila embryo and the more slowly developing and large Carausius morosus system. In relation to the issue of the importance of developmental and environmental constraints in biological evolution, still the missing link in current evolutionary thinking, insects and space facilities for long-term experiments could provide useful experimental settings where to critically assess how development and evolution may be interconnected. Finally, it has to be pointed out that since there are experimental data indicating a possible synergism between microgravity and space radiation, possible effects of space radiation should be taken into account in the planning and evaluation of experiments designed to test the potential role of microgravity on biological developmental and evolution.

Genome organization of Artemia mitochondrial DNA

To extend to the crustacean class the information concerning the genomic organization of the mitochondrial DNA (mtDNA) a double strategy has been used: Southern blot analysis with cloned Drosophila mtDNA probes and sequence comparison to the Drosophila mtDNA of the sequenced termini of different subclones along the Artemia mitochondrial genome, probably the smallest mtDNA studied at this level to date. These approaches have allowed us to localize the 16S rRNA gene, two tRNA genes and eleven protein genes. The genome organization is surprisingly similar to the Drosophila mtDNA, with the 16S rRNA and the protein genes located in the same positions and orientations as their Drosophila counterparts. The only changes detected are at the level of tRNA genes, although the position and orientation of some of these are also conserved. These results contrast with the important rearrangements detected among other invertebrates mtDNAs and suggest that the genome organization of the mitochondrial DNA may be more conserved in the arthropods than in other invertebrate phyla.