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Séminaires Micalis



Groupe à 5 ans Régulation spatiale des génomes

Institut Pasteur, Paris


Genomic analysis of microbial populations in their natural environment remains limited by the difficulty to assemble full genomes of individual species. Consequently, the chromosome organization of microorganisms has been investigated in a few model organisms, but the extent to which the features described can be generalized to other species remains unknown. Using controlled mixes of bacterial and yeast species, we developed meta3C, a high-throughput chromosome conformation capture experiment that allows characterizing individual genomes within a metagenome and their average chromosome organization. Not only can meta3C libraries be used on species with sequenced genomes, but the reads can also be used for the de novo assembly, scaffolding and 3D characterization of unknown genomes, providing an elegant and integrated approach to metagenomic analysis. Focusing on one of these species, Bacillus subtilis, we then combined super-resolution microscopy and high-resolution 3C to unravel the higher-order organization and dynamic rearrangements of its chromosome. Our results shed new light on the general principles underlying chromosome folding, and suggest that sub-megabase chromosomal structures may be evolutionary conserved.


Marbouty et al., “Meta3C unveils the diversity of chromosome organization in microorganisms”, eLife, 2014
Marie-Nelly et al., “High-quality genome (re)assembly from chromosome contact data”, Nature Communications, 2014
Marbouty et al., “3D folding mechanisms of higher-order chromatin domains”, in review

Lundi 02 février 2015 – 14h
Bâtiment 440 - Amphithéâtre J. Poly


Leyla Slamti – Equipe GME

01 34 65 23 82


Jean-Michel JAULT


7 Passage du Vercors 69367 Lyon cedex 07


Although the resistance to antibiotic is often multifaceted, multidrug transporters are now recognized as a major player in this mechanism and in particular in the onset of this phenomenon. One family of bacterial multidrug transporters belongs to the ABC (“ATP-Binding Cassette”) superfamily and they expel drugs at the expense of ATP hydrolysis.

In this presentation, I will summarize our effort to understand the functioning mechanism of two prototypical bacterial multidrug ABC transporters: one called BmrA from the model organism Bacillus subtilis and a second one from S/, PatA/PatB, which is involved in the resistance to fluoroquinolones. Both transporters are routinely overexpressed in E. coli, purified in high yield and reconstituted in liposomes or in nanodisks and are characterized by various biophysical and biochemical approaches.

Vendredi 06 février 2015 – 14h
Bâtiment 440 - Amphithéâtre J. Poly


Delphine Lechardeur – Equipe MicrobAdapt

01 34 65 23 95


Jean-Philippe NOUGAYREDE


CHU Purpan,  BP 3028, 31024 Toulouse, Cedex 03


Escherichia coli is a commensal inhabitant of the lower gastrointestinal tract of humans where it is the predominant facultative anaerobic organism. E. coli also belongs to the initial microbiota that colonizes the mammalian gut. Infants are stably colonized by E. coli within a few days after birth. Certain E. coli strains display enhanced ability to cause infection outside the intestinal tract. These extra-intestinal pathogenic E. coli (ExPEC) carry specific genetic determinants or virulence factors that are clustered on genomic islands. We have shown that a subset of ExPEC isolates harbor a genomic island, the pks island, which codes for the production of colibactin, a polyketide-non ribosomal peptide genotoxin. Colibactin production is not restricted to E. coli strains isolated from extra-intestinal infections. Commensal E. coli strains harboring the pks island are ubiquitous in the urban population of industrialized countries. Studies have focused on the impact of colibactin on host cells in vitro and in vivo. The production of colibactin was indeed demonstrated to generate DNA double strand breaks and host cell cycle arrest. Moreover, we recently showed that renewal of the mature intestinal epithelium depends on neonate gut residents and how critical is the synthesis of colibactin by commensal E. coli strain colonizing the newborn. Recent data also indicate that pks+ E. coli strains induce genomic instability and cellular senescence, which could induce carcinogenesis. On the other hand, we have also shown that the pks island is required for the colonic anti-inflammatory properties of a clinically efficient probiotic that is used empirically since almost one century (E. coli Nissle 1917). This Yin-Yang effect of colibactin could result from the production of heterogeneous compounds with different biological activities by the pks island-encoded biosynthetic pathway.

Mercredi 11 mars 2015 – 11h
Bâtiment 440 - Amphithéâtre J. Poly


Pascale Serror – Equipe CPE

01 34 65 21 66


Yves V. BRUN

Indiana University, Bloomington, IN, USA


The diversity of shapes of organisms is one of the most fascinating aspects in the field of biology. While bacteria display a myriad of morphologies, the mechanisms that control morphogenesis and the evolution of bacterial morphology are not understood. I will describe the mechanisms that control morphological diversity in species related to Caulobacter crescentus that synthesize appendage-like extensions of the cell envelope at distinct sub-cellular positions. I will show that stepwise evolution of a specific domain of a developmental regulator led to the gain of a new function and localization of this protein, which drove the sequential transition in morphology. Our results indicate that evolution of protein function, co-option, and modularity are key elements in the evolution of bacterial morphology (1). In addition, I will show how evolutionary consideration of the mechanism of growth in the alphaproteobacteria led to the surprising discovery that polar growth, rather than the previously assumed binary fission, is the predominant mode of growth in a large group of the alphaproteobacteria that includes the plant pathogen Agrobacterium tumefaciens and the human pathogen Brucella abortus (2). Finally, I will describe new methods of peptidoglycan labeling that allow the detection of sites of peptidoglycan synthesis in live cells and in real time, and their use to study the mechanisms of peptidoglycan synthesis and to show for the first time that pathogenic Chlamydia have peptidoglycan, ending 50 years of speculation and debate concerning the chlamydial anomaly (3, 4).


1. C. Jiang, P.J.B. Brown, A. Ducret, and Y.V. Brun. 2014. Sequential evolution of bacterial morphology by co-option of a developmental regulator. Nature, 506, 489-93.

2. Brown, P.J.B., M.A. de Pedro, D.T. Kysela, C. Van der Henst, J. Kim, X. De Bolle, C. Fuqua, and Y.V. Brun. 2012. Polar growth in the Alphaproteobacterial Order Rhizobiales. PNAS, 109: 1697-1701.

3. Kuru, E., H.V. Hughes, P.J.B. Brown, E. Hall, S. Tekkam, F. Cava, M.A. de Pedro, Y.V. Brun, and M.S. VanNieuwenhze. 2012. In situ Probing of Newly Synthesized Peptidoglycan in Live Bacteria with Fluorescent D-Amino Acids. Angewandte Chemie, 51(50):12519-23.

4. G. Liechti, E. Kuru, E. Hall, A. Kalinda, Y.V. Brun, M. VanNieuwenhze, and A. Maurelli. 2014. A new metabolic cell wall labeling method reveals peptidoglycan in Chlamydia trachomatis. Nature, 506, 507-10.

Jeudi 12 mars 2015 – 14h
Bâtiment 440 - Amphithéâtre J. Poly


Rut Carballido-Lopez – Equipe PROCED

01 34 65 29 55



Institut Curie, INSERM U932, Paris, F-75248 France


Macrophages are key components of the innate immune system and are part of the first line defense of the body. Killing intracellular pathogens is a key function of macrophages but many intracellular bacterial pathogens preferentially replicate in macrophage. In addition, macrophages represent one of the very few cellular targets of HIV. We are interested in the relationship between macrophages and HIV, studying the dynamics of the cycle of HIV in these immune cells as well as the response of the macrophages to the virus. We will review our recent progress regarding the cell biology of this complex host-pathogen relationship.


Bèrre, S., et al. (2013). CD36-specific antibodies block release of HIV-1 from infected primary macrophages and its transmission to T cells. J. Exp. Med. 210, 2523–2538. (cover image)

Gaudin, R., et al. (2013a). HIV trafficking in host cells: motors wanted! Trends in Cell Biology. 23, 652–662.

Gaudin, R., et al. (2013b). Dynamics of HIV-Containing Compartments in Macrophages Reveal Sequestration of Virions and Transient Surface Connections. PLoS ONE 8, e69450.

Gaudin, R., et al. (2012). Critical role for the kinesin KIF3A in the HIV life cycle in primary human macrophages. J Cell Biol 199, 467-479. (Featured article and cover image)

Jouve, M., et al. (2007) HIV-1 buds and accumulates in “non-acidic” endosomes of macrophages. Cell host & microbe. 2 : 85-95

Vendredi 20 mars 2015 – 14h
Bâtiment 440 - Amphithéâtre J. Poly


Nalini Rama Rao – Equipe Microbadapt

01 34 65 28 63


Christine Cavazza

Laboratoire de chimie et Biologie des Métaux

iRTSV-CEA Grenoble


In human pathogenic bacteria, nickel is required for the activation of two enzymes, urease and [NiFe]-hydrogenase, necessary for host infection. Acquisition of Ni(II) is mediated by either permeases or ABC-importers, the latter including a subclass that involves an

Extracytoplasmic nickel-binding protein, Ni-BP. Recently, we reported the structures of four Ni-BPs from a diversity of human pathogens, and revealed the existence of three new nickel-binding motifs. These are different from that previously described for E. coli Ni-BP NikA, known to bind nickel via a nickelophore, and indicate a variegated ligand selectivity for Ni-BPs. This study challenges the hypothesis of a general requirement of nickelophores for nickel uptake by canonical ABC-importers. Phylogenetic analyses showed that Ni-BPs have different evolutionary origins and emerged independently from peptide-binding proteins, possibly explaining the promiscuous behavior of this class of Ni(II) carriers.


Novel insights into nickel import in Staphylococcus aureus: the positive role of free histidine and structural characterization of a new thiazolidine-type nickel chelator. Lebrette H, et al. Metallomics. 2015 Jan 22 (in press)

Photocatalytic hydrogen production using polymeric carbon nitride with a hydrogenase and a bioinspired synthetic Ni catalyst. Caputo CA, et al. Angew Chem Int Ed Engl. 2014 Oct 20;53(43):11538-42

Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins. Lebrette H, et al. Structure. 2014 Oct 7;22(10):1421-32

Cobaloxime-based artificial hydrogenases. Bacchi M, et al. Inorg Chem. 2014 Aug 4;53(15):8071-82.

Common themes and unique proteins for the uptake and trafficking of nickel, a metal essential for the virulence of Helicobacter pylori. de Reuse H, Vinella D, Cavazza C. Front Cell Infect Microbiol. 2013 Dec 9;3:94.

Vendredi 3 avril 2015 – 14h
Bâtiment 440 - Amphithéâtre J. Poly


Elise Borézée-Durant – Equipe Microbadapt

01 34 65 23 95


Javier Pizarro-Cerda

Unite des Intéractions Bactéries-Cellules



Our group investigates the molecular internalization pathways of Listeria monocytogenes within host human cells. From a systems biology perspective, we have applied in recent years high-throughput screens of small-interfering RNA, microRNA as well as drug libraries which have identified novel signaling cascades which either promote or restrict L. monocytogenes infection. We have also revisited the contribution of major cytoskeletal effectors (including the Arp2/3 complex) to the full cell infection process. At present, we are expanding our research program towards the study of the cellular and in vivo infection strategies of epidemic L. monocytogenes strains, which harbor poorly characterized virulence factors that favor unsuspected bacterial interactions with its environment.


Genome-Wide siRNA Screen Identifies Complementary Signaling Pathways Involved in Listeria Infection and Reveals Different Actin Nucleation Mechanisms during Listeria Cell Invasion and Actin Comet Tail Formation. Kühbacher A, et al. MBio. 2015 May 19;6(3). pii: e00598-15.

The Legionella Kinase LegK2 Targets the ARP2/3 Complex To Inhibit Actin Nucleation on Phagosomes and Allow Bacterial Evasion of the Late Endocytic Pathway. Michard C, et al. MBio. 2015 May 5;6(3). pii: e00354-15.

Protein composition of the outermost exosporium-like layer of Clostridium difficile 630 spores. Díaz-González F, et al. J Proteomics. 2015 Jun 18;123:1-13.

Simultaneous analysis of large-scale RNAi screens for pathogen entry. Rämö P, et al. BMC Genomics. 2014 Dec 22;15:1162.

Phosphoinositides and host-pathogen interactions. Pizarro-Cerdá J, et al. Biochim Biophys Acta. 2015 Jun;1851(6):911-918.

Vendredi 12 juin 2015 – 14h
Bâtiment 440 - Amphithéâtre J. Poly


Hélène Bierne – Equipe EpiMic

01 34 65 22 89


Andrea Villarino

Section Biochimie, Université des Sciences et Techniques de Montevideo



Several evidences show that bacterial and viral PTPs act as virulence factors dephosphorylating eukaryotic proteins critical to cell cycle, altering metabolic and/or inflammatory responses of cells. Our interest is focused on the functional characterization of two PTPs of intracellular pathogens:  PtpA of Mycobacterium tuberculosis, and the only PTP of the Orf virus.

Mycobacterium tuberculosis (Mtb) is the causal agent of tuberculosis (TB) an infectious disease responsible for over 1.7 million human deaths every year. The bacterial PtpA is a key virulence factor released by Mycobacterium tuberculosis in the cytosol of infected macrophages. PtpA shows 37% of sequence identity and high structural similarity to its human orthologue HCPTPB. Our group recently identified four novel putative PtpA substrates, all related to energy metabolism: three mitochondrial proteins - the trifunctional enzyme, the ATP synthase, and the sulfide quinone oxidoreductase - and the cytosolic 6-phosphofructokinase. These substrates were isolated by an improved methodology to pull down novel PtpA substrates from an enriched P-Y macrophage extract, using the mutant PtpA D126A.  By different approaches we are addressing the validation of these proteins candidates as PtpA substrates.

The Orf virus is responsible for contagious pustular dermatitis disease of sheep, goats and humans. The viral PTP Orf has a 40% sequence homology with the VH1 phosphatase of Vaccinia virus, crucial for the viability and replication of the viral particle, and the blocking of interferon gamma signaling in the host. Our work seeks to characterize the Orf virus phosphatase to go through elucidate its role during the viral infection. By an in silico and experimental approach we demonstrated that the Orf phosphatase is a dimer in solution involving the amino terminal region, and the essentiality of the Cys 112 for the activity.

We believe that our work may contribute to understanding which is the role of PTP in pathogen adaptation to host macrophages, and at the same time, it sheds light into novel targets of eukaryotic orthologue phosphatases, as HCPTPB.



Mardi 16 juin 2015 – 11h
Bâtiment 440 - Amphithéâtre J. Poly


Gwenaelle André-Leroux – MaIAGE

01 34 65 22 64


Malcolm Watford

Department of Nutritional Sciences, Rutgers University,

New Brunswick, NJ 08901, USA


Adipocytes express very high glutamine synthetase (GS) activity and during the differentiation of both mouse 3T3 L1 cells and human pre-adipocytes into adipocytes GS protein content is induced many fold. GS protein was barely detectable in 3T3-L1 pre-adipocytes but increased rapidly during the first 24h of differentiation reaching a maximum by 72h. Knockdown of GS prevented differentiation unless exogenous glutamine was provided.  Early differentiation events, phosphorylation of ERK1/2 and down regulation of GADD153/CHOP10 did not require glutamine but monoclonal expansion and expression of C/EBPb, PPARg and C/EBPa were glutamine dependent.  RAW264.7 macrophage cells express extremely low levels of GS and have an absolute requirement for exogenous glutamine for survival.  RAW264.7 cells survive in the absence of exogenous glutamine when cultured over mature 3T3-L1 adipocytes, but do not survive in the absence of added glutamine when cultured over 3T3-L1 pre-adipocytes or mature 3T3-L1 adipocytes where GS has been knocked down.  Co-culture of mature 3T3-L1 adipocytes with RAW264.7 cells decreases CCL11/Eotaxin and MIP 1a production but increases IL6, MCP 1, CXCL1/KC, and CCL5/RANTES production, with the highest amounts detected when adipocyte GS is functional.  We propose that during obesity adipocyte synthesized glutamine is important to maintain adipocyte health but also provides fuel for the increased macrophage population and the subsequent development of insulin resistance.


Glutamine and glutamate supplementation raise milk glutamine concentrations in lactating gilts.Manso et al. J Anim Sci Biotechnol. 2012 Feb 28;3(1):2

A to Z of nutritional supplements: dietary supplements, sports nutrition foods and ergogenic aids for health and performance: part 32. Phillips SM, et al. Br J Sports Med. 2012 May;46(6):454-6

Protein. Watford M, Wu G. Adv Nutr. 2011 Jan;2(1):62-3.

mardi 23 juin 2015 – 14h
Bâtiment 442 - Auditorium A (RDJ)


Claire Cherbuy – Equipe Probihôte

01 34 65 24 98

Rédaction : rs
Date de création : 02 Avril 2011
Mise à jour : 05 Juin 2015