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- - - - - - - - - - - - New publications of the Department- - - - - - - - - - - -


Most of the antibiotics in current use are produced by Streptomyces species, Gram + filamentous bacteria living in the superficial layers of the soil. The team " Energetic Metabolism of Streptomyces" (MES) of the "Microbiology" department of I2BC tries to determine in which context these bioactive molecules are being produced and what are their functions for the producing bacteria.
Their studies demonstrated that phosphate limitation is a major trigger of antibiotics biosynthesis (1). Under such conditions of energy stress (ATP deficit), various processes are being triggered in order to restore the energetic balance of the cell. These include the up-regualtion of the expression of enzymes generating reduced co-factors (NADH) including those belonging to the TriCarboxylic Acid cycle (TCA) as the re-oxidation of NADH by the respiratory chain generates ATP. Such activation of the TCA cycle and thus of "oxidative phosphorylation" requires intensive fueling of the TCA by acetyl-CoA. Consequently, high antibiotic producing strains usually contain little or no storage lipids of the TriAcylGlycerol (TAG) family since the synthesis of these neutral lipids also requires acetyl-CoA (2). However, a strong activation of "oxidative phosphorylation" that results into high ATP generation cannot proceed in a situation of phosphate scarcity. Such situation would cause a dysfunction of the respiratory chain leading to the generation of reactive oxygen and nitrogen species (ROS and NOS) that are thought to constitute signals triggering antibiotics biosynthesis. Some antibiotics (Type I) would create damage to the membrane resulting into lysis of a fraction of the population to provide nutriments and especially phosphate to the surviving population (3). Other antibiotics (Type II) would reduce the electron flow of the respiratory chain via their ability to capture electrons in order to adjust and reduce ATP generation to low phosphate availability (2, 3). Doing so, they would also combat oxidative stress (1, 3). Finally, the last type of antibiotic (Type III) would inhibit various ATP consuming anabolic processes (cell wall/membrane, proteins, nucleic acids synthesis) to save ATP in conditions of phosphate scarcity (3). These three types of antibiotics target different cellular processes but they would all be involved in the regulation of the energetic metabolism of the bacterium in conditions of phosphate limitation / scarcity (3).
The endogenous roles proposed for the antibiotics and their traditionally proposed exogenous role of weapons conferring competitiveness in their ecological niche constitute simply the two sides of the same coin (3). Indeed these molecules are similarly toxic for their producer and for micro-organisms of the environnement, but the very strict temporal control of their biosynthesis and the induction of resistance determinants limit their toxicity to a very short period in the producer. In contrast, environmental microorganisms are likely to be sensitive to these harmful molecules, since they do not possess similar resistance mechanisms as the producing strains do (3).

(1) Millan-Oropeza et al., 2020 Scientific Reports
(2) Esnault et al., 2017 Scientific Reports
(3) Virolle 2020
see Scoop.It Life Sciences Université Paris-Saclay for a french version of this summary


Des membres du Département de Microbiologie engagés dans la lutte contre le Covid-19

La très grande majorité des membres du département sont confinés chez eux et poursuivent leurs activités de recherche et d’enseignement par télétravail.
L’équipe Endotoxines, Structures et Réponses de l’Hôte est engagée en première ligne dans la lutte contre le Covid-19. Le Pr. Pierre Tissières, chef du service réanimation pédiatrique et néonatale à l’Hôpital Bicêtre, le Pr. Florence Doucet-Populaire et le Dr. Nadège Bourgeois-Nicolaos, du service Bactériologie Hygiène à l’Hôpital-Béclère, sont en première ligne dans cette bataille sanitaire sans précédent. Ils soignent les malades en service de soins intensifs et sont impliqués dans le dépistage du coronavirus.

Merci pour leur implication et leur dévouement.

Leur message à nous tous : respectez l’isolement car c’est une maladie vraiment très contagieuse et vraiment sévère, sans commune mesure avec la grippe saisonnière.


- - - - New publication of the Department in Molecular Microbiology - - - -

9 April 2020 - The team of Nicolas Bayan published the paper entitled "The C-terminal domain of Corynebacterium glutamicum mycoloyltransferase A is composed of five repeated motifs involved in cell wall binding and stability" in Molecular Microbiology. Dietrich et al. Mol. Microbiol. 2020 Feb 19. doi : 10.1111/mmi.14492.

The genomes of Mycobacteria and related species contain several genes encoding mycoloyltransferases that are specific cell envelope enzymes essential for the biogenesis of the outer membrane. We determined the crystal structure of the major mycoloyltransferase MytA of Corynebacterium glutamicum and found that its C-terminal domain forms a stalk composed of five repeated LGFP motifs (4-stranded beta-fold) that interact specifically with the cell wall peptidoglycan-arabinogalactan polymer and contribute to the overall stability of the cell envelope. This is the first characterization of a specific carbohydrate binding motif identified in cell wall proteins of M. tuberculosis and related bacteria.


- - - - - - - - New publication of the Department in ISME Journal - - - - - - - -

1 April 2020 - Burkholderia insecticola triggers midgut closure in the bean bug Riptortus pedestris to prevent secondary bacterial infections of midgut crypts

Symbioses with beneficial microbes are essential for the normal growth of organisms. How organisms maintain these specific mutualisms is a fundamental question. In many symbioses, hosts acquire their specific symbionts from the environment every new generation, requiring sophisticated mechanisms to winnow out the desired bacteria from the large diversity of environmental bacteria. The symbiosis between the insect Riptortus pedestris and its gut symbiont Burkholderia insecticola is one of the model systems that is studied by researchers of the Microbiology Department of I2BC to understand how specificity in mutualistic interactions is maintained.

This insect houses its symbiont in a specific region of the gut composed of crypts that are fully occupied with millions of these bacteria. It uses different strategies to make sure that only the right symbiont occupies these crypts. One of them is a very strict check at the entrance of the crypt region, allowing only those bacteria with the right “ticket” to pass the gate. A second mechanism is based on competition between bacteria in the crypts leading to the efficient elimination of any contaminating bacteria that managed anyhow to enter despite the control at the entrance. In a new study published this March in the ISME Journal, the I2BC researchers, in collaboration with a Japanese team, have identified an additional feature enabling the insect to keep exclusivity for the symbiont in the crypts. Spatiotemporal microscopic observations of the infection process with bacteria labelled with a fluorescent protein revealed that after the initial passage of symbionts through the gate of the crypt region, it closes very rapidly and permanently, blocking any potential subsequent entry of unwanted microbes. This work thus expands the understanding of how animals sustain specific gut symbiosis.

The symbiotic crypt region of the insect intestine is occupied with a “red” symbiont. The “green” symbiont which was administered a few hours after the “red” one can not enter the crypt region because the gate was closed immediately after the entry of the red strain.


- - - - - - New publication of the Department in Scientific Reports - - - - - -

Natural products are an inexhaustible source of bioactive compounds for the pharmacopoeia. Among them, prenylated indole diketopiperazines exhibit various biological activities, including antibacterial, insecticidal, anticancer and immunomodulatory. They derive from the condensation of tryptophan with another amino acid and are produced mainly by filamentous fungi. However, the isolation of these compounds from the producing host is often difficult or impossible because of the uncontrolled conditions of production.

In a recent publication in Scientific Reports, the team Enzymology and Non Ribosomal Peptide Biosynthesis (I2BC/CEA) in collaboration with the SIMOPRO (CEA) and the Laboratory of Biomolecules (Sorbonne University) described the controlled production of prenylated indole diketopiperazines by the bacterium Escherichia coli. By using synthetic biology approaches, the authors associated genes encoding bacterial cyclodipeptide synthases (CDPSs) involved in building the core of the molecules and fungal prenyl transferases (PTs) that catalyze the anchoring of a prenyl group to the indole moiety of the tryptophan-containing cyclodipeptides. In addition, the authors showed that the production of prenylated indole diketopiperazines was increased by the expression in bacteria of seven other genes encoding a recombinant pathway for dimethylallyl diphosphate (DMAPP), a PT substrate essential for the transfer of the prenyl group (Figure 1). Of the 11 CDPS/PT tested combinations, seven were found to be effective for the production of prenylated indole diketopiperazines that were purified and characterized by NMR spectroscopy. This work illustrates the potential of synthetic biology for the production of new bioactive compounds in a tractable chassis by using enzyme combinations not found in nature.

Figure 1 : Schematic representation of an Escherichia coli bacterium programmed for the production of prenylated indole diketopiperazines. CDPSs use aminoacylated tRNAs (aa-tRNA) to produce cyclodipeptides which are then prenylated by PTs. This latter reaction is enhanced when the intracellular pool of DMAPP (shown in orange) is increased. The prenylated indole diketopiperazines are recovered from the culture medium. Glu-3P, glucose-3-phosphate.

- - - - - - - - - - - - - - - New member of the department - - - - - - - - - - - - - - - -

We are pleased to welcome Johann Peltier who has just been recruited as an Assistant Professor at Paris-Sud University and will join the “Regulatory RNAs in Clostridia” team in September 2019.
Congratulations to Johann for this performance !


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Congratulations to Emma Piattelli for getting the PhD fellowship to start her PhD thesis in October 2019 in the « Regulatory RNAs in Clostridia” team under the supervision of Pr Olga Soutourina. Welcome to Emma and good luck for her work on the role of non-coding RNAs in the pathogenesis of Clostridium difficile.


- - - - - - - - - - I2BC Microbiology Department Meeting 2019 - - - - - - - - - - -

The yearly I2BC Microbiology Department Meeting will be held on Friday June 7th in the Auditiorium of Bât. 21 in Gif-sur-Yvette (CNRS campus).

The theme of this year is “Microbiology and Health” with the following four sessions :

1) Biotechnology and Health
2) Horizontal Gene Transfer/Antibiotic Resistance/Gut Microbiota
3) Biology of Pathogens
4) Innate Immunity

Download the detailed program :

For inscription (free !), click here.
Please indicate your participation to the morning session, lunch (offered by the Department) and afternoon session. You also have the possibility to present a Poster. Please send us by e-mail to Peter Mergaert or Nicolas Mirouze your Poster Abstract. Be sure to use your e-mail address in the doodle so that we can send you updates of the program.

We are looking forward to see you in the meeting,

The Microbiology Department


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MICROBES DAY.........still time to register !!!!!!! !

For the first time, we organized an inter Paris-Saclay laboratories meeting around Microbiology. The Paris-Saclay MICROBES day, held on Wednesday March 27th 2019 at Gif-sur-Yvette, will showcase the diversity of Microbiology research performed at Paris-Saclay University. This event gathers a community of experts exploring the multiple facets of Microbiology (bacteria, archaea, microbial eukaryotes & viruses) across all scales : from molecules to genes, genomes, cells, populations, communities, and from basic sciences to applied innovations in microbial and molecular engineering and from environmental to human health.

Session 1 : Microbial ecology and evolution

Session 2 : From molecules to microbial cells

Session 3 : Molecular and microbial engineering

Session 4 : Host-microbes interactions and health microbiology

more info :


- - - - - - New publication of the Department in New Phytologist - - - - - - -

17 January 2019 - The biotrophic pathogen Agrobacterium tumefaciens genetically transforms plants and thereby induces the formation of plant tumors which constitute a specific niche for the pathogen. In a paper recently published on-line in The New Phytologist (The biotroph Agrobacterium tumefaciens thrives in tumors by exploiting a wide spectrum of plant host metabolites Almudena Gonzalez‐Mula, Joy Lachat ,Léo Mathias Delphine Naquin Florian Lamouche Peter Mergaert Denis Faure), Denis Faure and his colleagues described how the pathogen mobilizes its central metabolism for exploiting a wide diversity of nutrient resources present in the tumor.

A combination of omics revealed some metabolic pathways involved in the plant host exploitation by the biotroph Agrobacterium tumefaciens.

The diversity and abundance of plant metabolites in plant tumors was characterized by metabolomics, and then transposon-sequencing and transcriptomics were used for identifying the Agrobacterium key-genes involved in the exploitation of some metabolites as a source of nutrients. Finally, reverse genetics allowed to verify the role of these genes in aggressiveness and fitness of Agrobacterium when it colonizes the plant tumors. This work highlights how a biotroph mobilizes its central metabolism for exploiting a wide diversity of resources in plant host. It further shows the complementarity of functional genome-wide scans by transcriptomics and transposon-sequencing to decipher the lifestyle of a plant pathogen.


- - - - - - - - Master of Fundamental Microbiology of Paris Saclay - - - - - - -

Our 2018-2019 class propose a digest of recent articles in Microbiology

1- Nicolas Alexandre : Insights in Bdellovibrio bacteriovorus predation

2- Emile Auria : Bacteriophages cooperation

3- Kimberley Casado : Cohabitation with the enemy !

4- Nicolas Ducrot : Co-production of therapeutic drugs by yeast

5- Antony Goudin : Giant viruses

6- Virgile Gueneau : Pathogen elimination by probiotic Bacillus

7- Hugo Guerin : Electrical communication in bacterial communities

8- Gaetan Pavard : Control of dormancy in Cyanobacteria

9- Emma Piattelli : Engineering bacteria to eradicate Malaria

10- Marius Poulain : Symbiosis in marine sponges

11- Gabriella Sarango : Bacteria-electronic devices for health

12- Louise Sibleyras : Bacterial Prions

13- Léa Swistak : OMVs and toxin delivery

- - - - - - - - - - - Have a nice reading and ....... Happy 2019 !!! - - - - - - - - - - -


- - - - New publication of the Department in Nature Communications - - -

30 November 2018 - In a paper published today online in Nature Communications, the Mirouze team report that wall teichoic acids (WTAs), cell wall-anchored anionic glycopolymers associated to numerous critical functions in Gram-positive bacteria, are involved in this initial step of transformation. Using a combination of cell wall-targeting antibiotics and fluorescence microscopy, the team show that competence-specific WTAs are produced and specifically localized in the competent cells to mediate DNA binding at the proximity of the transformation apparatus. On the basis of their results and previous knowledge in the field, they propose a new model for DNA binding and transport during genetic transformation in B. subtilis.


- - - - - - - - - The International Balzan Prize for Eva Kondorosi - - - - - - - - -

23 November 2018 - Today, Eva Kondorosi, former member of the Plant-Bacteria Interactions group of the department, received out of the hands of the President of the Italian Republic the Balzan Prize for Chemical Ecology.
Eva made the largest part of her carreer as a CNRS researcher, first in the ISV and then in the I2BC. Presently she is in the Biological Research Center of the Hungarian Academy of Sciences in Szeged, Hungary.
She received the award for her lifelong work on understanding the symbiosis between legume plants and soil bacteria known as rhizobia. Eva Kondorosi is renowned for her work on dissecting this interaction ; identifying the Rhizobium nodulation genes whose products, the Nod factors, trigger nodule development and bacterial infection in the host plant and discovering hundreds of nodule cysteine-rich plant peptides which are important signaling molecules and effectors of the differentiation of endosymbionts.


- - - - - - - - - - - - - - - - - - - Fête de la science 2018 - - - - - - - - - - - - - - - - - - -

15 October 2018


- - - Adam Kondorosi Academia Europaea Award for Peter Mergaert - - -

30 August 2018 - Peter Mergaert receives this year’s Adam Kondorosi Academia Europaea Award for Early Career Investigators for his work on bacterial differentiation during the Rhizobium-legume symbiosis. He received the prize during the 13th European Nitrogen Fixation Conference in Stockholm this august.

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