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See detailDiscrimination of deciduous tree species from time series of unmanned aerial system imagery
Lisein, Jonathan ULiege; Michez, Adrien ULiege; Claessens, Hugues ULiege et al

in PLoS ONE (2015), 10(11),

Technology advances can revolutionize Precision Forestry by providing accurate and fine forest information at tree level. This paper addresses the question of how and particularly when Unmanned Aerial ... [more ▼]

Technology advances can revolutionize Precision Forestry by providing accurate and fine forest information at tree level. This paper addresses the question of how and particularly when Unmanned Aerial System (UAS) should be used in order to efficiently discriminate deciduous tree species. A time series of high resolution UAS imagery was collected to cover the growing season from leaf flush to leaf fall. Full benefit was taken of the temporal resolution of UAS acquisition, one of the most promising features of small drones. The disparity in forest tree phenology is at the maximum during early spring and late autumn. But the phenology state that optimized the classification result is the one that minimizes the spectral variation within tree species groups and, at the same time, maximizes the phenologic differences between species. Sunlit tree crowns (5 deciduous species groups) were classified using a Random Forest approach for monotemporal, two-date and three-date combinations. The end of leaf flushing was the most efficient single-date time window. Multitemporal datasets definitely improve the overall classification accuracy. But single-date high resolution orthophotomosaics, acquired on optimal time-windows, result in a very good classification accuracy (overall out of bag error of 16%). [less ▲]

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See detailWood Specific Gravity Variations and Biomass of Central African Tree Species: The Simple Choice of the Outer Wood
Bastin, Jean-François ULiege; Fayolle, Adeline ULiege; Tarelkin, Yegor et al

in PLoS ONE (2015)

Context: Wood specific gravity is a key element in tropical forest ecology. It integrates many aspects of tree mechanical properties and functioning and is an important predictor of tree biomass. Wood ... [more ▼]

Context: Wood specific gravity is a key element in tropical forest ecology. It integrates many aspects of tree mechanical properties and functioning and is an important predictor of tree biomass. Wood specific gravity varies widely among and within species and also within individual trees. Notably, contrasted patterns of radial variation of wood specific gravity have been demonstrated and related to regeneration guilds (light demanding vs. shade-bearing). However, although being repeatedly invoked as a potential source of error when estimating the biomass of trees, both intraspecific and radial variations remain little studied. In this study we characterized detailed pith-to-bark wood specific gravity profiles among contrasted species prominently contributing to the biomass of the forest, i.e., the dominant species, and we quantified the consequences of such variations on the biomass. Methods: Radial profiles of wood density at 8% moisture content were compiled for 14 dominant species in the Democratic Republic of Congo, adapting a unique 3D X-ray scanning technique at very high spatial resolution on core samples. Mean wood density estimates were validated by water displacement measurements. Wood density profiles were converted to wood specific gravity and linear mixed models were used to decompose the radial variance. Potential errors in biomass estimation were assessed by comparing the biomass estimated from the wood specific gravity measured from pith-to-bark profiles, from global repositories, and from partial information (outer wood or inner wood). Results: Wood specific gravity profiles from pith-to-bark presented positive, neutral and negative trends. Positive trends mainly characterized light-demanding species, increasing up to 1.8 g.cm-3 per meter for Piptadeniastrum africanum, and negative trends characterized shade-bearing species, decreasing up to 1 g.cm-3 per meter for Strombosia pustulata. The linear mixed model showed the greater part of wood specific gravity variance was explained by species only (45%) followed by a redundant part between species and regeneration guilds (36%). Despite substantial variation in wood specific gravity profiles among species and regeneration guilds, we found that values from the outer wood were strongly correlated to values from the whole profile, without any significant bias. In addition, we found that wood specific gravity from the DRYAD global repository may strongly differ depending on the species (up to 40% for Dialium pachyphyllum). Main conclusion: Therefore, when estimating forest biomass in specific sites, we recommend the systematic collection of outer wood samples on dominant species. This should prevent the main errors in biomass estimations resulting from wood specific gravity and allow for the collection of new information to explore the intraspecific variation of mechanical properties of trees. [less ▲]

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See detailEctopic Expression of Retrotransposon-Derived PEG11/RTL1 Contributes to the Callipyge Muscular Hypertrophy.
Xu, Xuewen; Ectors, Fabien ULiege; Davis, Erica E. et al

in PloS one (2015), 10(10), 0140594

The callipyge phenotype is an ovine muscular hypertrophy characterized by polar overdominance: only heterozygous +Mat/CLPGPat animals receiving the CLPG mutation from their father express the phenotype ... [more ▼]

The callipyge phenotype is an ovine muscular hypertrophy characterized by polar overdominance: only heterozygous +Mat/CLPGPat animals receiving the CLPG mutation from their father express the phenotype. +Mat/CLPGPat animals are characterized by postnatal, ectopic expression of Delta-like 1 homologue (DLK1) and Paternally expressed gene 11/Retrotransposon-like 1 (PEG11/RTL1) proteins in skeletal muscle. We showed previously in transgenic mice that ectopic expression of DLK1 alone induces a muscular hypertrophy, hence demonstrating a role for DLK1 in determining the callipyge hypertrophy. We herein describe newly generated transgenic mice that ectopically express PEG11 in skeletal muscle, and show that they also exhibit a muscular hypertrophy phenotype. Our data suggest that both DLK1 and PEG11 act together in causing the muscular hypertrophy of callipyge sheep. [less ▲]

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See detailA lysine cluster in domain II of Bacillus subtilis PBP4a plays a role in the membrane attachment of this C1-PBP
Vanden Broeck, Arnaud; Van Der Heiden, Edwige ULiege; Sauvage, Eric ULiege et al

in PLoS ONE (2015)

In PBP4a, a Bacillus subtilis class-C1 penicillin-binding protein (PBP), four clustered lysine (K) residues, K86, K114, K119, and K265, protrude from domain II. Replacement of these amino acids with ... [more ▼]

In PBP4a, a Bacillus subtilis class-C1 penicillin-binding protein (PBP), four clustered lysine (K) residues, K86, K114, K119, and K265, protrude from domain II. Replacement of these amino acids with glutamine (Q) residues by site-directed mutagenesis yielded Mut4KQ PBP4a. When produced in Escherichia coli without its predicted Sec-signal peptide, wildtype (WT) PBP4a was found mainly associated with the host cytoplasmic membrane, whereas Mut4KQ PBP4a remained largely unbound. After purification, the capacities of the two proteins to bind to B. subtilis membranes were compared. The results were similar to those obtained in E. coli: in vitro, a much higher percentage of WT PBP4a than of Mut4KQ PBP4a was found to interact with B. subtilis membranes. Immunodetection of PBP4a in B. subtilis membrane extracts revealed that a processed form of this PBP (as indicated by its size) associates with the B. subtilis cytoplasmic membrane. In the absence of any amphiphilic peptide in PBP4a, the crown of positive charges on the surface of domain II is likely responsible for the cellular localization of this PBP and its attachment to the cytoplasmic membrane. [less ▲]

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See detailTemporal and spatial comparisons of underwater sound signatures of different reef habitats in Moorea Island, French Polynesia
Bertucci, Frédéric; Parmentier, Eric ULiege; Berten, Laetitia et al

in PLoS ONE (2015)

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See detailA semiquantitative framework for gene regulatory networks: increasing the time and quantitative resolution of Boolean networks
Kerkhofs, Johan ULiege; Geris, Liesbet ULiege

in PLoS ONE (2015), 10(6), 0130033

Boolean models have been instrumental in predicting general features of gene networks and more recently also as explorative tools in specific biological applications. In this study we introduce a basic ... [more ▼]

Boolean models have been instrumental in predicting general features of gene networks and more recently also as explorative tools in specific biological applications. In this study we introduce a basic quantitative and a limited time resolution to a discrete (Boolean) framework. Quantitative resolution is improved through the employ of normalized variables in unison with an additive approach. Increased time resolution stems from the introduction of two distinct priority classes. Through the implementation of a previously published chondrocyte network and T helper cell network, we show that this addition of quantitative and time resolution broadens the scope of biological behaviour that can be captured by the models. Specifically, the quantitative resolution readily allows models to discern qualitative differences in dosage response to growth factors. The limited time resolution, in turn, can influence the reachability of attractors, delineating the likely long term system behaviour. Importantly, the information required for implementation of these features, such as the nature of an interaction, is typically obtainable from the literature. Nonetheless, a trade-off is always present between additional computational cost of this approach and the likelihood of extending the model’s scope. Indeed, in some cases the inclusion of these features does not yield additional insight. This framework, incorporating increased and readily available time and semi-quantitative resolution, can help in substantiating the litmus test of dynamics for gene networks, firstly by excluding unlikely dynamics and secondly by refining falsifiable predictions on qualitative behaviour. [less ▲]

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See detailChitosan enriched three-dimensional matrix reduces inflammatory and catabolic mediators production by human chondrocytes
Oprenyeszk, Frédéric ULiege; Sanchez, Christelle ULiege; Dubuc, Jean-Emile et al

in PLoS ONE (2015), 10(5),

This in vitro study investigated the metabolism of human osteoarthritic (OA) chondrocytes encapsulated in a spherical matrix enriched of chitosan. Human OA chondrocytes were encapsulated and cultured for ... [more ▼]

This in vitro study investigated the metabolism of human osteoarthritic (OA) chondrocytes encapsulated in a spherical matrix enriched of chitosan. Human OA chondrocytes were encapsulated and cultured for 28 days either in chitosan-alginate beads or in alginate beads. The beads were formed by slowly passed dropwise either the chitosan 0.6%- alginate 1.2% or the alginate 1.2% solution through a syringe into a 102 mM CaCl2 solution. Beads were analyzed histologically after 28 days. Interleukin (IL)-6 and -8, prostaglandin (PG) E2, matrix metalloproteinases (MMPs), hyaluronan and aggrecan were quantified directly in the culture supernatant by specific ELISA and nitric oxide (NO) by using a colorimetric method based on the Griess reaction. Hematoxylin and eosin staining showed that chitosan was homogeneously distributed through the matrix and was in direct contact with chondrocytes. The production of IL-6, IL-8 and MMP-3 by chondrocytes significantly decreased in chitosan-alginate beads compared to alginate beads. PGE2 and NO decreased also significantly but only during the first three days of culture. Hyaluronan and aggrecan production tended to increase in chitosan-alginate beads after 28 days of culture. Chitosan-alginate beads reduced the production of inflammatory and catabolic mediators by OA chondrocytes and tended to stimulate the synthesis of cartilage matrix components. These particular effects indicate that chitosan-alginate beads are an interesting scaffold for chondrocytes encapsulation before transplantation to repair cartilage defects. [less ▲]

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See detailEmployees' Organizational Identification and Affective Organizational Commitment: An integrative approach
Stinglhamber, Florence; Marique, Géraldine; Caesens, Gaëtane et al

in PLoS ONE (2015), 10(4), 0123955

Although several studies have empirically supported the distinction between organizational identification (OI) and affective commitment (AC), there is still disagreement regarding how they are related ... [more ▼]

Although several studies have empirically supported the distinction between organizational identification (OI) and affective commitment (AC), there is still disagreement regarding how they are related. Precisely, little attention has been given to the direction of causality between these two constructs and as to why they have common antecedents and outcomes. This research was designed to fill these gaps. Using a cross-lagged panel design with two measurement times, Study 1 examined the directionality of the relationship between OI and AC, and showed that OI is positively related to temporal change in AC, confirming the antecedence of OI on AC. Using a cross-sectional design, Study 2 investigated the mediating role of OI in the relationship between three work experiences (i.e., perceived organizational support, leader-member exchange, and job autonomy) and AC, and found that OI partially mediates the influence of work experiences on AC. Finally, Study 3 examined longitudinally how OI and AC combine in the prediction of actual turnover, and showed that AC totally mediates the relationship between OI and turnover. Overall, these findings suggest that favorable work experiences operate via OI to increase employees' AC that, in turn, decreases employee turnover. [less ▲]

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See detailHigh Resolution postontrast time of flight MR angiography of intracranial perforators at 7.0 Tesla
Harteveld, A; de Cocker, L; Dieleman, N et al

in PLoS ONE (2015)

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See detailRetirement age and the age of onset of Alzheimer’s disease: Results from the ICTUS study
Grotz, Catherine ULiege; Letenneur, Luc; Bonsang, Eric ULiege et al

in PLoS ONE (2015), 10(2), 0115056

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See detailThe Psychometric Properties of the French Version of the Personality Inventory for DSM- 5
Roskam, I.; Galdiolo, S.; Hansenne, Michel ULiege et al

in PLoS ONE (2015), 10(7),

In the context of the publication of DSM-5, the Personality Inventory for DSM-5 (PID-5) has been proposed as a new dimensional assessment tool for personality disorders. This instrument includes a pool of ... [more ▼]

In the context of the publication of DSM-5, the Personality Inventory for DSM-5 (PID-5) has been proposed as a new dimensional assessment tool for personality disorders. This instrument includes a pool of 220 items organized around 25 facets included in a five-factor second- order domain structure. The examination of the replicability of the trait structure across methods and populations is of primary importance. In view of this need, the main objective of the current study was to validate the French version of the PID-5 among French-speaking adults from a European community sample (N=2,532). In particular, the assumption of unidimensionality of the 25 facet and the five domain scales was tested, as well as the extent to which the five-factor structure of the PID-5 and the DSM-5 personality trait hierarchical structure are replicated in the current sample. The results support the assumption of unidimensionality of both the facets and the domains. Exploratory factor and hierarchical analyses replicated the five-factor structure as initially proposed in the PID-5. © 2015 Roskam et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. [less ▲]

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See detailGenome-Wide Analysis of In Vivo Binding of the Master Regulator DasR in Streptomyces coelicolor Identifies Novel Non-Canonical Targets
Świątek-Połatyńska, MA; Bucca, G; Laing, E et al

in PLoS ONE (2015)

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See detailEstimation of canine leishmania infection prevalence in six cities of the algerian littoral zone using a bayesian approach
Amel, A; Abatih, E; Speybroeck, N et al

in PLoS ONE (2015), 10(3),

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See detailQuality of Antimicrobial Products Used in Striped Catfish (Pangasianodon hypophthalmus) Aquaculture in Vietnam.
Tran Minh Phu; Nguyen Than Phuong; Scippo, Marie-Louise ULiege et al

in PLoS ONE (2015), 10

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See detailCharacterization of Proteinuria in Dogue de Bordeaux Dogs, a Breed Predisposed to a Familial Glomerulonephropathy: A Retrospective Study.
Lavoue, Rachel; Trumel, Catherine; Smets, Pascale M. Y. et al

in PLoS ONE (2015), 10(7), 0133311

Dogue de Bordeaux dog has been reported to be predisposed to a familial glomerulonephropathy that displays some morphological modifications reported in focal and segmental glomerulosclerosis. Prevalence ... [more ▼]

Dogue de Bordeaux dog has been reported to be predisposed to a familial glomerulonephropathy that displays some morphological modifications reported in focal and segmental glomerulosclerosis. Prevalence of quantitatively abnormal renal proteinuria was recently reported to be 33% in this breed. The nature of the proteinuria was assessed by sodium dodecyl sulfate-agarose gel electrophoresis and determinations of urinary markers (urinary retinol-binding protein, urinary N-acetyl-beta-glucosaminidase, urinary albumin and urinary immunoglobulin G) on stored specimens. Diagnostic performances of sodium dodecyl sulfate-agarose gel electrophoresis to identify dogs with elevated urinary biomarkers were assessed. Samples from 102 adult Dogue de Bordeaux dogs (47 non-proteinuric [urine protein-to-creatinine ratio </= 0.2], 20 borderline-proteinuric [0.2< urine protein-to-creatinine ratio </= 0.5] and 35 proteinuric dogs [urine protein-to-creatinine ratio >0.5]) were used, of which 2 were suffering from familial glomerulonephropathy. The electrophoretic protein patterns, for all but one proteinuric dog, were indicative of a glomerular origin and, in all dogs, the urinary albumin concentration related to creatinine concentration and the urinary immunoglobulin G concentration related to creatinine concentration were above the upper limit of the reference interval established for the breed. Sensitivity and specificity of sodium dodecyl sulfate-agarose gel electrophoresis identifying dogs with elevated urinary albumin concentration were 94% and 92%, respectively, while diagnostic performance of sodium dodecyl sulfate-agarose gel electrophoresis in detecting dogs with elevated urinary immunoglobulin G concentration yielded sensitivity and specificity of 90% and 74%, respectively. These results suggest that all proteinuric and some borderline-proteinuric Dogue de Bordeaux dogs likely have underlying glomerular lesions and that sodium dodecyl sulfate-agarose gel electrophoresis and urinary markers might be useful to screen dogs with borderline-proteinuria. Additional investigations are warranted to assess if these findings are related to the familial glomerulonephropathy. [less ▲]

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See detailIndividual Monitoring of Immune Response in Atlantic Salmon Salmo salar following Experimental Infection with Infectious Salmon Anaemia Virus (ISAV).
Collet, Bertrand; Urquhart, Katy; Mira Monte, Milena ULiege et al

in PLoS ONE (2015), 10(9), 0137767

Monitoring the immune response in fish over the progression of a disease is traditionally carried out by experimental infection whereby animals are killed at regular intervals and samples taken. We ... [more ▼]

Monitoring the immune response in fish over the progression of a disease is traditionally carried out by experimental infection whereby animals are killed at regular intervals and samples taken. We describe here a novel approach to infectiology for salmonid fish where blood samples are collected repeatedly in a small group of PIT-tagged animals. This approach contributes to the reduction of animals used in research and to improved data quality. Two groups of 12 PIT-tagged Atlantic salmon (Salmo salar) were i.p infected with Infectious Salmon Anaemia Virus (ISAV) or culture medium and placed in 1 m3 tanks. Blood samples were collected at 0, 4, 8, 12, 16, 21 and 25 days post infection. The viral load, immune and stress response were determined in individual fish by real-time quantitative PCR (QPCR) on the blood cells, as well as the haematocrit used as an indicator of haemolysis, a clinical consequence of ISAV infection. "In-tank" anaesthesia was used in order to reduce the stress related to chase and netting prior to sampling. The data were analysed using a statistical approach which is novel with respect to its use in fish immunology. The repeated blood collection procedure did not induce stress response as measured by HSP70 and HSP90 gene expression in the un-infected animals. A strong increase in viraemia as well as a significant induction of Mx and gammaIP gene expression were observed in the infected group. Interleukin 10 was found induced at the later stage of the infection whereas no induction of CD8 or gamma IFN could be detected. These results and the advantages of this approach are discussed. [less ▲]

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See detailAnatomically discrete sex differences in neuroplasticity in zebra finches as reflected by perineuronal nets.
Cornez, Gilles ULiege; Ter Haar, Sita M.; Cornil, Charlotte ULiege et al

in PloS one (2015), 10(4), 0123199

Large morphological sex differences in the vertebrate brain were initially identified in song control nuclei of oscines. Besides gross differences between volumes of nuclei in males and females, sex ... [more ▼]

Large morphological sex differences in the vertebrate brain were initially identified in song control nuclei of oscines. Besides gross differences between volumes of nuclei in males and females, sex differences also concern the size and dendritic arborization of neurons and various neurochemical markers, such as the calcium-binding protein parvalbumin (PV). Perineuronal nets (PNN) of the extracellular matrix are aggregates of different compounds, mainly chondroitin sulfate proteoglycans, that surround subsets of neurons, often expressing PV. PNN develop in zebra finches song control nuclei around the end of the sensitive period for song learning and tutor deprivation, known to delay the end of the song learning sensitive period, decreases the numbers of PNN in HVC. We demonstrate here the existence in zebra finches of a major sex difference (males > females) affecting the number of PNN (especially those surrounding PV-positive cells) in HVC and to a smaller extent the robust nucleus of the arcopallium, RA, the two main nuclei controlling song production. These differences were not present in Area X and LMAN, the lateral magnocellular nucleus of the anterior nidopallium. A dense expression of material immunoreactive for chondroitin sulfate was also detected in several nuclei of the auditory and visual pathways. This material was often organized in perineuronal rings but quantification of these PNN did not reveal any sex difference with the exception that the percentage of PNN surrounding PV-ir cells in the dorsal lateral mesencephalic nucleus, MLd, was larger in females than in males, a sex difference in the opposite direction compared to what is seen in HVC and RA. These data confirm and extend previous studies demonstrating the sex difference affecting PNN in HVC-RA by showing that this sex difference is anatomically specific and does not concern visual or auditory pathways. [less ▲]

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See detailThe Interferon-Inducible Mouse Apolipoprotein L9 and Prohibitins Cooperate to Restrict Theiler's Virus Replication.
Kreit, Marguerite; Vertommen, Didier; Gillet, Laurent ULiege et al

in PloS one (2015), 10(7), 0133190

Apolipoprotein L9b (Apol9b) is an interferon-stimulated gene (ISG) that has antiviral activity and is weakly expressed in primary mouse neurons as compared to other cell types. Here, we show that both ... [more ▼]

Apolipoprotein L9b (Apol9b) is an interferon-stimulated gene (ISG) that has antiviral activity and is weakly expressed in primary mouse neurons as compared to other cell types. Here, we show that both Apol9 isoforms (Apol9b and Apol9a) inhibit replication of Theiler's murine encephalomyelitis virus (TMEV) but not replication of vesicular stomatitis virus (VSV), Murid herpesvirus-4 (MuHV-4), or infection by a lentiviral vector. Apol9 genes are strongly expressed in mouse liver and, to a lesser extent, in pancreas, adipose tissue and intestine. Their expression is increased by type I interferon and viral infection. In contrast to genuine apolipoproteins that are involved in lipid transport, ApoL9 has an intracytoplasmic localization and does not seem to be secreted. The cytoplasmic localization of ApoL9 is in line with the observation that ApoL9 inhibits the replication step of TMEV infection. In contrast to human ApoL6, ApoL9 did not sensitize cells to apoptosis, in spite of the presence of a conserved putative BH3 domain, required for antiviral activity. ApoL9a and b isoforms interact with cellular prohibitin 1 (Phb1) and prohibitin 2 (Phb2) and this interaction might contribute to ApoL9 antiviral activity. Knocking down Phb2 slightly increased TMEV replication, irrespective of ApoL9 overexpression. The antiviral activity of prohibitins against TMEV contrasts with the pro-viral activity of prohibitins observed for VSV and reported previously for Dengue 2 (DENV-2), Chikungunya (CHIKV) and influenza H5N1 viruses. ApoL9 is thus an example of ISG displaying a narrow antiviral range, which likely acts in complex with prohibitins to restrict TMEV replication. [less ▲]

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See detailStreptococcus pneumoniae GAPDH Is Released by Cell Lysis and Interacts with Peptidoglycan.
Terrasse, Remi; Amoroso, Ana Maria ULiege; Vernet, Thierry et al

in PloS one (2015), 10(4), 0125377

Release of conserved cytoplasmic proteins is widely spread among Gram-positive and Gram-negative bacteria. Because these proteins display additional functions when located at the bacterial surface, they ... [more ▼]

Release of conserved cytoplasmic proteins is widely spread among Gram-positive and Gram-negative bacteria. Because these proteins display additional functions when located at the bacterial surface, they have been qualified as moonlighting proteins. The GAPDH is a glycolytic enzyme which plays an important role in the virulence processes of pathogenic microorganisms like bacterial invasion and host immune system modulation. However, GAPDH, like other moonlighting proteins, cannot be secreted through active secretion systems since they do not contain an N-terminal predicted signal peptide. In this work, we investigated the mechanism of GAPDH export and surface retention in Streptococcus pneumoniae, a major human pathogen. We addressed the role of the major autolysin LytA in the delivery process of GAPDH to the cell surface. Pneumococcal lysis is abolished in the DeltalytA mutant strain or when 1% choline chloride is added in the culture media. We showed that these conditions induce a marked reduction in the amount of surface-associated GAPDH. These data suggest that the presence of GAPDH at the surface of pneumococcal cells depends on the LytA-mediated lysis of a fraction of the cell population. Moreover, we demonstrated that pneumococcal GAPDH binds to the bacterial cell wall independently of the presence of the teichoic acids component, supporting peptidoglycan as a ligand to surface GAPDH. Finally, we showed that peptidoglycan-associated GAPDH recruits C1q from human serum but does not activate the complement pathway. [less ▲]

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