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Imelio JA, Trajtenberg F, Mondino S, Zarantonelli L, Vitrenko I, Lemée L, Cokelaer T, Picardeau M, Buschiazzo A. Signal-sensing triggers the shutdown of HemKR, regulating heme and iron metabolism in the spirochete Leptospira biflexa. PLoS One 2024; 19:e0311040. [PMID: 39325783 PMCID: PMC11426443 DOI: 10.1371/journal.pone.0311040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024] Open
Abstract
Heme and iron metabolic pathways are highly intertwined, both compounds being essential for key biological processes, yet becoming toxic if overabundant. Their concentrations are exquisitely regulated, including via dedicated two-component systems (TCSs) that sense signals and regulate adaptive responses. HemKR is a TCS present in both saprophytic and pathogenic Leptospira species, involved in the control of heme metabolism. However, the molecular means by which HemKR is switched on/off in a signal-dependent way, are still unknown. Moreover, a comprehensive list of HemKR-regulated genes, potentially overlapped with iron-responsive targets, is also missing. Using the saprophytic species Leptospira biflexa as a model, we now show that 5-aminolevulinic acid (ALA) triggers the shutdown of the HemKR pathway in live cells, and does so by stimulating the phosphatase activity of HemK towards phosphorylated HemR. Phospho~HemR dephosphorylation leads to differential expression of multiple genes, including of heme metabolism and transport systems. Besides the heme-biosynthetic genes hemA and the catabolic hmuO, which we had previously reported as phospho~HemR targets, we now extend the regulon identifying additional genes. Finally, we discover that HemR inactivation brings about an iron-deficit tolerant phenotype, synergistically with iron-responsive signaling systems. Future studies with pathogenic Leptospira will be able to confirm whether such tolerance to iron deprivation is conserved among Leptospira spp., in which case HemKR could play a vital role during infection where available iron is scarce. In sum, HemKR responds to abundance of porphyrin metabolites by shutting down and controlling heme homeostasis, while also contributing to integrate the regulation of heme and iron metabolism in the L. biflexa spirochete model.
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Pipoli da Fonseca J, Kornobis E, Turc E, Enouf V, Lemée L, Cokelaer T, Monot M. Capturing SARS-CoV-2 from patient samples with low viral abundance: a comparative analysis. Sci Rep 2022; 12:19274. [PMID: 36369470 PMCID: PMC9652350 DOI: 10.1038/s41598-022-23422-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Since the beginning of the SARS-CoV-2 coronavirus pandemic, genome sequencing is essential to monitor viral mutations over time and by territory. This need for complete genetic information is further reinforced by the rapid spread of variants of concern. In this paper, we assess the ability of the hybridization technique, Capture-Seq, to detect the SARS-CoV-2 genome, either partially or in its integrity on patients samples. We studied 20 patient nasal swab samples broken down into five series of four samples of equivalent viral load from CT25 to CT36+ . For this, we tested 3 multi-virus panel as well as 2 SARS-CoV-2 only panels. The panels were chosen based on their specificity, global or specific, as well as their technological difference in the composition of the probes: ssRNA, ssDNA and dsDNA. The multi-virus panels are able to capture high-abundance targets but fail to capture the lowest-abundance targets, with a high percentage of off-target reads corresponding to the abundance of the host sequences. Both SARS-CoV-2-only panels were very effective, with high percentage of reads corresponding to the target. Overall, capture followed by sequencing is very effective for the study of SARS-CoV-2 in low-abundance patient samples and is suitable for samples with CT values up to 35.
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Najjar I, Motreff L, Ma L, Lemée L, Briolat V, Monot M. How Did Institut Pasteur's NGS Core Facility, Biomics, Manage the Coronavirus Disease 2019 Crisis? J Biomol Tech 2021; 32:50-56. [PMID: 34140839 DOI: 10.7171/jbt.21-3202-004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In 2020, research entities at the Institut Pasteur (IP) in Paris, as elsewhere around the world, were closed because of the coronavirus disease 2019 (COVID-19) pandemic. However, IP core facilities, laboratories, services, and departments working on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and priority projects were authorized to continue working both on site and remotely. Given the importance of its role in SARS-CoV-2 genome-sequencing initiatives, the IP Biomics core facility was fully functional during the first (i.e., March-June 2020) and second (i.e., November-December 2020) national lockdowns. We describe here how Biomics successfully implemented an emergency management plan to deal with this health crisis. We highlight the internal deployment of the institutional business continuity plan (BCP) through a series of actions. We also address the impact of the COVID-19 crisis on Biomics staff and collaborators. The added value of quality management and the limitations of risk management systems are discussed. Finally, we suggest that the Biomics infrastructure and the BCP described here could be used for benchmarking purposes, for other next-generation sequencing core facilities wishing to implement/improve their processes, and for future major crisis management.
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Musadji NY, Lemée L, Caner L, Porel G, Poinot P, Geffroy-Rodier C. Spectral characteristics of soil dissolved organic matter: Long-term effects of exogenous organic matter on soil organic matter and spatial-temporal changes. CHEMOSPHERE 2020; 240:124808. [PMID: 31546188 DOI: 10.1016/j.chemosphere.2019.124808] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
The aim of this study was to evaluate the long-term effect of urban and green waste compost exogenous organic matter (EOM) on soil dissolved organic matter (DOM). A luvic cambisol was amended 7 years before the study. DOM was investigated along a soil profile down to 1 m depth regarding seasonal variations (autumn and spring). DOM sampled by suction cups was characterized using dissolved organic carbon (DOC) content and excitation emission matrix (EEM) fluorescence. The variability of DOM concentrations was pronounced but no major change in composition was determined. The results obtained, reinforced by statistical analysis, showed that the DOM quality was mainly influenced by soil management (organic matter amendment) whereas the quantity mainly depended on the season (heavy precipitation event). DOM humic characteristics were strongly dependent on amendment and changed with depth but was not affected by the season. Long term effect of compost organic matter was highlighted after a 7-years amendment.
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Lahbib S, Leblond CS, Hamza M, Regnault B, Lemée L, Mathieu A, Jaouadi H, Mkaouar R, Youssef-Turki IB, Belhadj A, Kraoua I, Bourgeron T, Abdelhak S. Homozygous 2p11.2 deletion supports the implication of ELMOD3 in hearing loss and reveals the potential association of CAPG with ASD/ID etiology. J Appl Genet 2018; 60:49-56. [PMID: 30284680 DOI: 10.1007/s13353-018-0472-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 11/30/2022]
Abstract
Autism spectrum disorder (ASD) is a set of neurodevelopmental conditions characterized by early-onset difficulties in social communication and unusually restricted, repetitive behavior and interests. Parental consanguinity may lead to higher risk of ASD and to more severe clinical presentations in the offspring. Studies of ASD families with high inbreeding enable the identification of inherited variants of this disorder particularly those with an autosomal recessive pattern of inheritance. In our study, using copy number variants (CNV) analysis, we identified a rare homozygous deletion in 2p11.2 region that affects ELMOD3, CAPG, and SH2D6 genes in a boy with ASD, intellectual disability (ID), and hearing impairment (HI). This deletion may reveal a new contiguous deletion syndrome in which ELMOD3, known to be implicated in autosomal recessive deafness underlies the HI of the proband and CAPG, member of actin regulatory proteins involved in cytoskeletal dynamic, an important function for brain development and activity, underlies the ASD/ID phenotype. A possible contribution of SH2D6 gene, as a part of a chimeric gene, to the clinical presentation of the patient is discussed. Our result supports the implication of ELMOD3 in hearing loss and highlights the potential clinical relevance of 2p11.2 deletion in autism and/or intellectual disability.
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Dargère S, Parienti JJ, Roupie E, Gancel PE, Wiel E, Smaiti N, Loiez C, Joly LM, Lemée L, Pestel-Caron M, du Cheyron D, Verdon R, Leclercq R, Cattoir V. Unique blood culture for diagnosis of bloodstream infections in emergency departments: a prospective multicentre study. Clin Microbiol Infect 2014; 20:O920-7. [DOI: 10.1111/1469-0691.12656] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/29/2014] [Accepted: 04/23/2014] [Indexed: 11/30/2022]
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Liu F, Boissou F, Vignault A, Lemée L, Marinkovic S, Estrine B, De Oliveira Vigier K, Jérôme F. Conversion of wheat straw to furfural and levulinic acid in a concentrated aqueous solution of betaïne hydrochloride. RSC Adv 2014. [DOI: 10.1039/c4ra03878a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Caron F, Delbos V, Deghmane AE, Lemée L, Jeannot E, Houivet E, Taha MK. N-13: Immunogénicité à long terme du vaccin MenBvac en Seine-Maritime. Med Mal Infect 2014. [DOI: 10.1016/s0399-077x(14)70278-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Lemée L, Pinard L, Beauchet R, Kpogbemabou D. Evaluation of humic fractions potential to produce bio-oil through catalytic hydroliquefaction. BIORESOURCE TECHNOLOGY 2013; 149:465-469. [PMID: 24140851 DOI: 10.1016/j.biortech.2013.09.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/20/2013] [Accepted: 09/24/2013] [Indexed: 06/02/2023]
Abstract
Humic substances were extracted from biodegraded lignocellulosic biomass (LCBb) and submitted to catalytic hydroliquefaction. The resulting bio-oils were compared with those of the initial biomass. Compared to fulvic and humic acids, humin presented a high conversion rate (74 wt.%) and the highest amount of liquid fraction (66 wt.%). Moreover it represented 78% of LCBb. Humin produced 43 wt.% of crude oil and 33 wt.% of hexane soluble fraction containing hydrocarbons which is a higher yield than those from other humic substances as well as from the initial biomass. Hydrocarbons were mainly aromatics, but humin produces the highest amount of aliphatics. Considering the quantity, the quality and the molecular composition of the humic fractions, a classification of the potential of the latter to produce fuel using hydroliquefaction process can be assess: Hu>AF>AH. The higher heating value (HHV) and oxygen content of HSF from humin were fully compatible with biofuel characteristics.
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Lemoine F, Maupin I, Lemée L, Lavoie JM, Lemberton JL, Pouilloux Y, Pinard L. Alternative fuel production by catalytic hydroliquefaction of solid municipal wastes, primary sludges and microalgae. BIORESOURCE TECHNOLOGY 2013; 142:1-8. [PMID: 23732916 DOI: 10.1016/j.biortech.2013.04.123] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 04/29/2013] [Accepted: 04/30/2013] [Indexed: 06/02/2023]
Abstract
An alternative fuel production was investigated through catalytic hydroliquefaction of three different carbonaceous sources: solid municipal wastes (MW), primary sludges (PS), and microalgae (MA). The reaction was carried out under hydrogen pressure, at different temperatures (330, 380 and 450°C), with a Raney nickel catalyst and two different hydrogen donor solvents: a "fossil solvent" (tetralin) and a "green solvent" (2-methyl-hydro-furan). The feeds analyses (TDA-TGA, ICP-AES, lipids quantification) showed that MW and PS had similar characteristics and physico-chemical properties, but different from those of MA. The hydroliquefaction of these feeds allowed to obtain high oil yields, with a significant energetic value, similar to that of a bio-petroleum. 2-methyl-hydro-furan was more efficient than tetralin for the treatment of the strongly bio-degraded biomasses MW and PS, while better results were obtained with tetralin in the case of MA.
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Lemée L, Kpogbemabou D, Pinard L, Beauchet R, Laduranty J. Biological pretreatment for production of lignocellulosic biofuel. BIORESOURCE TECHNOLOGY 2012; 117:234-241. [PMID: 22617032 DOI: 10.1016/j.biortech.2012.04.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 06/01/2023]
Abstract
Lignocellulosic biomass was submitted to a biological pretreatment prior to a catalytic hydroliquefaction in order to produce biofuel. The biodegradation process was conducted over 3 months in a reactor under controlled conditions. During the biodegradation process the organic matter was characterised and its evolution was correlated with physico-chemical parameters. In parallel with the analysis of the lipidic fraction, analytical pyrolysis was used to monitor bacterial activity. The alterations of branched to linear fatty acids ratio and of mono- to diacids ratio were compared when determined by thermochemolysis and observed in the directly extractable lipids. The evolution of the phytol to the corresponding isoprenoic ketone ratio was observed to be dependent on the desorption technique since it decreases using headspace while it increases using pyrolysis. "Humic"/"fulvic acids" ratio, infrared spectroscopy and thermodifferential analysis were used to determine the degree of OM complexification.
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Pinto Cardoso G, Michelet I, Lemée L, Durand I, Caseris M, Mallet E, Marguet C. P463 - Premier cas d’endocardite à Moraxella caprae. Arch Pediatr 2010. [DOI: 10.1016/s0929-693x(10)70856-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Marguet C, Lemée L, Pin I, Le Roux E. Chest physiotherapy improved the detection of Pseudomonas aeruginosa in airway secretions from non expectorator CF children. J Cyst Fibros 2010. [DOI: 10.1016/s1569-1993(10)60118-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Som MP, Lemée L, Amblès A. Stability and maturity of a green waste and biowaste compost assessed on the basis of a molecular study using spectroscopy, thermal analysis, thermodesorption and thermochemolysis. BIORESOURCE TECHNOLOGY 2009; 100:4404-4416. [PMID: 19443212 DOI: 10.1016/j.biortech.2009.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 04/07/2009] [Accepted: 04/08/2009] [Indexed: 05/27/2023]
Abstract
The organic matter (OM) of a green waste and bio waste compost was characterised over 8months and the observed evolution was correlated with physico-chemical parameters (temperature, pH, carbon content, C/N ratio). Thermochemolysis and thermodesorption were used to monitor bacterial activity (stability) whereas diffuse reflectance infrared fourier transform spectroscopy (DRIFTS) and thermodifferential analysis (TDA) permitted to determine the degree of OM humification (maturity). DRIFT spectroscopy and TDA provide two indicators of maturity since, with these two techniques, the signals associated with the biodegradable organic matter decrease relatively to the signals associated with refractory organic matter. This increase in R(TG) and R(IR) ratios between aromatic to aliphatic signals constitutes a proof for OM complexification. It correlates with humic acids/fulvic acids ratio known to be a maturity index. Pyrolysates are mainly constituted of lignin moieties, terpenoids, nitrogen containing compounds, carbohydrates (furanosic moiety), mono- and diacids (as methyl esters), and methoxyesters. The R(branched/linear) ratio between branched to linear acids traduces the evolution of the bacterial activity during composting. Moreover the R(di/mono) ratio between aliphatic mono to diacids correlates with the latter showing that diacids can occur from the biological oxidation of monoacids. These two ratios determined by thermochemolysis are useful to monitor the stability of compost. VOC, observed by thermodesorption are mainly constituted of terpenes, light acids, aldehydes and ketone. An unexpected result was obtained since the amount of phytol increases relatively to the isoprenoid ketone considered to originate from the latter.
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Legru E, Lubrano M, Lemée L, Marguet C. [Acute RSV bronchiolitis: should we be looking for pertussis?]. Arch Pediatr 2009; 16:283-4. [PMID: 19186038 DOI: 10.1016/j.arcped.2008.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 04/15/2008] [Accepted: 12/11/2008] [Indexed: 11/27/2022]
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Lemée L. [What microbiological criteria define colonization or infection with Staphylococcus aureus and Pseudomonas aeruginosa]. Rev Mal Respir 2003; 20:S69-78. [PMID: 12910137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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Frebourg NB, Nouet D, Lemée L, Martin E, Lemeland JF. Comparison of ATB staph, rapid ATB staph, Vitek, and E-test methods for detection of oxacillin heteroresistance in staphylococci possessing mecA. J Clin Microbiol 1998; 36:52-7. [PMID: 9431919 PMCID: PMC124806 DOI: 10.1128/jcm.36.1.52-57.1998] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The performance characteristics of the E-test (AB Biodisk, Solna, Sweden), the ATB Staph, the Rapid ATB Staph, and the Vitek GPS-503 card (bioMérieux, La Balme Les Grottes, France) methods for the detection of oxacillin resistance in a collection of staphylococci with a high proportion of troublesome strains were evaluated. Sixty-four Staphylococcus aureus strains and 76 coagulase-negative staphylococcal strains were tested. All strains were mecA positive and were characterized by the oxacillin agar screen plate test; 75 (53.6%) were found to be heterogeneous by a large-inoculum oxacillin disk diffusion assay, and oxacillin MICs for 89 (63.6%) were < or = 32 microg/ml. Three (4.7%) S. aureus strains and 25 (32.9%) coagulase-negative strains were classified as susceptible by the E-test, as defined by the National Committee for Clinical Laboratory Standards (NCCLS) oxacillin breakpoint (MIC < or = 2 microg/ml). The ATB Staph method failed to detect oxacillin resistance in 7 (11%) S. aureus isolates and 32 (42.1%) coagulase-negative isolates. The MICs for all but six of these discrepant isolates were < or = 16 microg/ml. The Rapid ATB Staph method was tested against S. aureus strains only and yielded 15 (23.4%) false-susceptible results for strains for which the MICs were < or = 32 microg/ml. The Vitek system was the best-performing system, since it failed to detect oxacillin resistance in only 3 (4.7%) S. aureus strains and 15 (19.7%) coagulase-negative strains, the MICs for all of which were < or = 2 microg/ml. These data indicate that (i) the performance of the two ATB Staph systems can be limited when the prevalence of borderline-heteroresistant staphylococci is high and (ii) the unreliability of the E-test and the Vitek methods for detecting resistant coagulase-negative strains might be reduced by the potential revision of the oxacillin breakpoint currently recommended by the NCCLS.
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Lemée L, Hue G, Lavoinne A. [Concentration of creatine kinase MB mass: variability depending on the analytic system]. Ann Biol Clin (Paris) 1996; 54:381-2. [PMID: 9092307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Montaudon E, Lemée L, Bourgeois MJ. Synthèse de divers types d'hétérocycles fonctionnels par décomposition de peroxydes insaturés: réactions compétitives. CAN J CHEM 1995. [DOI: 10.1139/v95-024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Decomposition of γ-unsaturated substituted peroxides in a good hydrogen donor solvent can lead to two diastereoisomeric oxetans. An intramolecular 1,5 hydrogen shift followed by a cyclization may compete with the homolytic intramolecular substitution following the first addition step. The factors governing this never-reported competition are determined. Keywords: unsaturated peroxides, oxetans, homolytic intramolecular substitution, intramolecular 1,5 hydrogen shift.
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