I2BC Paris-Saclay

Nitrogen, cell wall and osmotic stresses are intimately linked in S. coelicolor and the aggravation of these stresses leads to an increase of antibiotic biosynthesis.

Streptomyces coelicolor and Streptomyces lividans constitute model strains to study the regulation of antibiotics biosynthesis in Streptomyces species since these closely related strains possess the same pathways directing the biosynthesis of various antibiotics but only S. coelicolor expresses them. To get a better understanding of the origin of the contrasted abilities of these strains to produce bioactive specialized metabolites, these strains were grown in conditions of phosphate limitation or proficiency and a comparative analysis of their transcriptional and regulatory proteins was carried out. The abundance of the vast majority of the 355 proteins detected greatly
differed between these two strains and responded differently to phosphate availability. This study confirmed, consistently with previous studies, that S. coelicolor suffers from nitrogen stress. This stress likely triggers the degradation of the nitrogen-rich peptidoglycan cell wall in order to recycle nitrogenpresent in its constituents, resulting in cell wall stress. An altered cell wall being unable to fulfil its osmo-protective function, the bacteria also suffers from osmotic stress. This study thus revealed that these three stresses are intimately linked in S. coelicolor. The aggravation of these stresses being known to lead to an increase in antibiotics biosynthesis, an explanatory
model of the links existing between these stresses and the production of antibiotics is proposed.

More information: https://www.mdpi.com/1422-0067/23/23/14792

Contact: Marie-Joëlle Virolle <marie-joelle.virolle@i2bc.paris-saclay.fr>

The gut symbiont Caballeronia insecticola triggers epithelial stem cell proliferation and inhibits apoptosis to coordinate gut morphology and create an exclusive colonization niche in the gut of the plant pest insect Riptortus pedestris. 

The insect Riptortus pedestris, a pest species of soybean, harbors in its gut the specific bacterial symbiont Caballeronia insecticola, which stimulates insect development, fertility and immunity. The symbiont colonizes the posterior midgut region that is composed of hundreds of crypts. Before colonization, the midgut crypts are primordial with their epithelial cells closely aligned leaving little or no lumen between them. Colonization by C. insecticola triggers a swift opening of the crypts creating a large luminal cavity that is subsequently entirely filled by the symbiont. We analyzed the fate of crypt epithelial cells to understand the mechanism of the symbiont-mediated crypt development. Intestinal stem cells (ICSs) are located and proliferate at the base of the crypts. Differentiated enterocytes migrate upward along the epithelial cell layers of the crypts and enterocyte apoptosis primarily occurred on the tip side of the crypts. Apoptotic cells were then eventually shed from the crypts into the hemolymph. In symbiont-free, aposymbiotic crypts, the proliferation rate of the stem cells at the base of the crypts was low while the apoptotic rate was high at the crypt tips, resulting in the primordial, closed aposymbiotic crypt morphology. On the other hand, infecting C. insecticola promoted the proliferation rate of the stem cells at the base of crypts and simultaneously inhibited apoptosis at the tip of crypts to very low levels, resulting in a net growth of the crypts and the generation of a crypt lumen that becomes colonized by the bacterial symbiont. We speculate that the Caballeronia symbiont infection generates molecular signals that finely regulate the enterocyte cell cycle, enabling the creation of a symbiont niche and the specific colonization of the cryps.

More information: https://www.frontiersin.org/articles/10.3389/fphys.2022.1071987/full

Contact: Peter Mergaert (peter.mergaert@i2bc.paris-saclay.fr)

We performed the first-time engineering and comparative analysis of the best studied cyanobacterium Synechocystis PCC6803 for the photosynthetic production of five chemically high-value terpenes: from CO2 (biofuels, flavors) and water (even polluted).

Cyanobacteria, “microalgae” that colonise most of our planet’s ecosystems, have the potential for the sustainable production of carbon compounds from solar energy, water (even polluted) and CO2. We focused on the production of terpenes, high-value, volatile compounds (no energy required to harvest and break the biomass that produces them) that have a pleasant odour and a high energetic density. Hence terpenes can be used for the production of drugs, flavors, fragrances, solvents and/or biofuels. We have performed the first-time engineering and comparative analysis of the best-studied cyanobacterium Synechocystis PCC 6803 for the photosynthetic production of five chemically diverse high-value terpenes: two monoterpenes (C10H16) limonene (cyclic molecule) and pinene (bicyclic), and three sesquiterpenes (C15H24) bisabolene (cyclic), farnesene (linear) and santalene (cyclic). All terpene producers appeared to grow well and to be genetically stable. We showed that Synechocystis PCC 6803 can efficiently and stably produce farnesene and santalene, which had never been produced before by this model organism or any other cyanobacteria, respectively. We have also shown for the first time that Synechocystis is able to produce terpenes efficiently, when nitrate, the classical nitrogen source of cyanobacteria, is replaced by urea (cheaper than nitrate) to save costs of future industrial production or to combine production and depollution. Very interestingly, our results indicate, that Synechocystis is more proficient at producing sesquiterpenes (C15H24) than monoterpenes (C10H16), for reasons we currently investigate.

More information: https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-022-02211-0

Contact: Franck Chauvat <franck.chauvat@i2bc.paris-saclay.fr>

An art project to pay tribute to the laboratory mouse, often sacrificed on the altar of science.

More information: here

Contact: Sylvie Lautru <sylvie.lautru@i2bc.paris-saclay.fr>

Single horizonal gene transfer explains the emergence of DNA gyrase in Archaea.

DNA gyrase is a type II topoisomerase with the unique capacity to introduce negative supercoiling in DNA. In bacteria, DNA gyrase has an essential role in the homeostatic regulation of supercoiling. While ubiquitous in Bacteria, DNA gyrase was previously reported to have a patchy distribution in Archaea but its emergent function and evolutionary history in this domain of life remains elusive. In this study, we used phylogenomic approaches and an up-to date sequence dataset to establish global and archaeaspecific phylogenies of DNA gyrases. The most parsimonious evolutionary scenario infers that DNA gyrase was introduced into the lineage leading to Euryarchaeal group II via a single horizontal gene transfer from a bacterial donor which we identified as an ancestor of Gracilicutes and/or Terrabacteria. The archaea-focused trees indicate that DNA gyrase spread from Euryarchaeal group II to some DPANN and Asgard lineages via rare horizontal gene transfers. The analysis of successful recent transfers suggests a requirement for syntropic or symbiotic/parasitic relationship between donor and recipient organisms. We further show that the ubiquitous archaeal Topoisomerase VI may have co-evolved with DNA gyrase to allow the division of labour in the management of topological constraints. Collectively, our study reveals the evolutionary history of DNA gyrase in Archaea and provides testable hypotheses to understand the prerequisites for successful establishment of DNA gyrase in a naïve archaeon and the associated adaptations in the management of topological constraints.

More information here

Contact: Tamara Basta <tamara.basta@i2bc.paris-saclay.fr>

The morning will be devoted to tributes and testimonials from people who have been fortunate enough to work with Mike Dubow during his teaching and research activities. The afternoon will be devoted to a symposium of the Department of Microbiology, which will focus on three scientific themes dear to Mike: extremophiles, biofilms and environmental phages.

Each theme will include a presentation by a member of the Department and an external collaborator.

Registration: https://evento.renater.fr/survey/hommage-a-michael-dubow-vendredi-30-septembre-2022-iary7xq2

Contact: hommage.mike@i2bc.paris-saclay.fr

Cyanobacteria contribute to biomineralization of Calcium carbonates over the geological history. By combining genomics and biochemistry, I2BC researchers and their collaborators discovered a new family of genes coding an enzyme (calcyanin) involved in the biomeneralization of cacium carbonates in cynobacteria.

We propose a new approach for Enterobacter species identification based on the diversity of the gene encoding the heat shock protein DnaJ. This new tool can be easily implemented in clinical laboratories in addition to identification by MALDI-TOF.

The taxonomy of the genus Enterobacter can be confusing and has been considerably revised in recent years. We propose a PCR and amplicon sequencing technique based on a partial sequence of the dnaJ gene for species assignment consistent with DNA-DNA digital hybridization (dDDH) and pairwise average nucleotide identity (ANI).We performed a validation of the method by comparing the type strains of each species, sequences obtained from the GenBank database, and clinical specimens. Our results show that the polymorphism of the target sequence of dnaJ allows the identification of species. Using this gene, we assigned the species to 100 strains deposited in the GenBank database that were consistent with the species assignment by dDDH and ANI. The analysis showed that using the partial dnaJ sequence is congruent with WGS as far as correct identification of Enterobacter species is concerned. Finally, we applied our dnaJ method on a national collection of 68 strains identified as Enterobacter isolated from the blood cultures of premature babies using an algorithm based on a type strain library and the SeqScape® software. For the first time, we identified Enterobacter quasihormaechei in blood cultures from four neonatal sepsis cases. We also noticed a higher prevalence of E. bugandensis (36.3%; 32/88) and E. xiangfangensis (46.5%; 41/88). E. bugandensis is a novel species recently described specifically in instances of neonatal sepsis. In conclusion, sequencing a part of the dnaJ gene could be a quick, more economical, and highly discriminating method of identifying Enterobacter species in clinical practice and research.

More information here.

Contact person: Nadege Bourgeois-Nicolaos

In this review in Current Opinion in Microbiology special issue, we discuss recent insights into the role of RNAs in modulating interactions between the emerging human enteropathogen C. difficile and phages in light of intriguing data in other prokaryotes.

Clostridioides difficile (formerly Clostridium difficile)-associated diarrhea is currently the most frequently occurring nosocomial diarrhea worldwide. During its infection cycle this pathogen needs to survive in phage-rich gut communities. Recent data strongly suggest that regulatory RNAs control gene expression in C. difficile and many of these RNAs appear to modulate C. difficile-phage interactions. Of the 200 regulatory RNAs identified by deep sequencing and targeted approaches, many function as antitoxins within type I toxin-antitoxin (TA) modules and CRISPR RNAs for anti-phage defenses. The purpose of this review is to give an overview of the RNAs contributing to the interactions of C. difficile with phages focusing on CRISPR-Cas and TA systems in light of intriguing recent data in other prokaryotes. We first describe what is known about the contribution of phages to C. difficile physiology and then highlight the recent findings on the emerging roles of RNAs in C. difficile-phage interactions. Open questions that arise from these first observations and future directions with potential roles of additional classes of regulatory RNAs are discussed. This increasing knowledge provides essential basis for future development of new molecular tools as well as promising diagnostic and therapeutic applications.

More information: https://doi.org/10.1016/j.mib.2021.11.012

Contact person: Olga Soutourina

Unveiling how bacteria modify the surface of solid walls in their close environment at the nanoscale is an important step in nanotechnology and bioengineering as well as in geomicrobiology and fundamental surface chemistry/physics.

Bacteria have evolved on earth for billions of years and have managed to colonize all ecological niches. Their metabolic diversity is so vast that they play a major role in the biogeochemical cycles of our planet. Understanding the mechanisms by which bacteria interact with the first interfacial layers of the solid matter that surrounds them is an important issue with many perspectives in both fundamental and applied science. Thin iron films, with a surface area of centimeters and a thickness of nanometers, have been produced. The nanofilm’s opacity being related to its thickness, it is then possible to measure both the nanofilm’s degradation and to localize and quantify the bacteria dynamics in situ and in real time by simple optical means (backgroud of the picture). This experimental work published in the journal ACS Central Science indicates a homogeneous corrosion of iron nanofilms triggered suddenly by bacteria. Experiments reveal in particular rapid motions of Shewanella oneidensis MR1 bacteria during iron dissolution. Mutants of S. oneidensis as well as other bacterial species such as E. coli and L. plantarum are also able to induce corrosion (figure). All the experiments highlight more generally the role of electroactive respiratory proteins and soluble secreted molecules in the modification of the surface properties of nanofilms.

More information here.

Contact person: Christophe Regeard

The GO Paris-Saclay 2021 team won a gold medal and the "Best Inclusivity" prize at the iGEM 2021 international synthetic biology competition on Sunday, November 14.

The team's project "EndoSeek" aims to develop a new diagnostic tool for endometriosis, which is a painful and poorly understood pathology caused by the proliferation of uterine cells outside the uterus. Worldwide, this disease affects about 10% of women and can take up to 7 years to diagnose. Based on preliminary studies using small patient cohorts, certain blood microRNAs (miRNAs) may be biomarkers of the disease.
The team has developed a machine learning program that will allow identification of new endometriosis biomarkers with future cohorts. In experiments conducted this summer at I2BC, students exploited Cas13a and Cas14a1 nucleases for miRNA detection. They created a video game to educate adults and children over the age of 10 about endometriosis and synthetic biology. Finally, following their dialogue with patients and physicians, they questioned the ethical implications of diagnostics.
The team was awarded the Best Inclusivity Award for outstanding efforts to include people with diverse identities. The students thought about the position of LGBT+ people in their project and created a multi-language, voice-assisted website with color customization.
This project was supported by the I2BC, the Faculty of Sciences of the University of Paris-Saclay, La Diagonale Paris-Saclay, EUGLOH (European University Alliance for Global Health), the Graduate School Life Sciences and Health, IDT and Promega.

Team 2021 supervisors included Téo Hébra (ICSN) and 5 members of the I2BC: Philippe Bouloc, Stéphanie Bury-Moné, Emma Piattelli, Ombeline Rossier and Charlène Valadon.
For more information, see the wiki https://2021.igem.org/Team:GO_Paris-Saclay and the video https://video.igem.org/w/ihqYR3UfveimEtZVv7x6jE.

How fast do swimming bacteria navigate toward oxygen and how does their speed relate to the oxygen concentration? These questions are explored using bacteria tracking in a glass capillary and in situ oxygen measurements.

Aerotaxis is the ability of motile cells to navigate toward oxygen. A key question is the dependence of the aerotactic velocity with the local oxygen concentration c. We combined simultaneous bacteria tracking and local oxygen concentration measurements using Ruthenium encapsulated in micelles to characterize the aerotactic response of Burkholderia contaminans, a motile bacterium ubiquitous in the environment. In our experiments, an oxygen gradient is produced by the bacterial respiration in a sealed glass capillary permeable to oxygen at one end, producing a bacterial band traveling toward the oxygen source. We compute the aerotactic response χ(c) both at the population scale, from the drift velocity in the bacterial band, and at the bacterial scale, from the angular modulation of the run times. Both methods are consistent with a power-law χ ∝ c−2, in good agreement with existing models based on the biochemistry of bacterial membrane receptors.

More information: https://journals.aps.org/pre/abstract/10.1103/PhysRevE.106.034404

Contact: Peter Mergaert (peter.mergaert@i2bc.paris-saclay.fr)

Location: Institute for Integrative Biology of the Cell (I2BC), Building 21, avenue de la Terrasse, 91190 Gif-sur-Yvette, France

Scientific context: Agrobacterium and its relatives have been fascinating the scientists for more than century. These bacteria evolved a unique capacity to genetically modify the infected plants to force them to become a welcoming host. From studies on the interaction processes between Agrobacterium and its hosts, exceptional scientific advances in biology and biotechnology have emerged and some others still occur today.

Objectives: Agrobacterium 2023 is a joint event of the 43rd American Crown gall meeting and the 4th European Agrobacterium Conference. This meeting will bring together French and international scientists working in all aspect of Agrobacterium biology: from basic science to applied fields in agronomy and genome editing technologies.

Topics:        Pathology: plant damage and protection
Host-microbes signaling: cell and genome reprograming
Genome biology: architecture, evolutionary biology and taxonomy
Cell biology and structural biology: molecular machineries
Genetic engineering: DNA delivery and recombination

Contact: Denis Faure <denis.faure@i2bc.paris-saclay.fr>

The morning was devoted to personal and scientific testimonies which highlighted Mike's imagination, insatiable curiosity and innovative ideas as well as his great popularity with students in France and abroad.

The afternoon was devoted to scientific presentations, around 3 themes that Mike was passionate about: biofilms, extremophilic bacteria and environmental phages.

These presentations were given by researchers from the department and by two guest researchers, Adrienne Kish (MNHN, Paris) and Romain Briandet (Institut Micalis, Jouy-en-Josas).

The over-expression of an atypical TetR regulator totally abolishes the production of antibiotics of the strong antibiotic producer, S. coelicolor.

Conditions of phosphate and nitrogen proficiency are known to strongly repress antibiotic biosynthesis in Streptomyces species. Consistently, S. coelicolor, a strain characterized by a poor ability to assimilate nitrogen and phosphate, produces abundantly antibiotics. The group MES characterized an atypical regulator of TetR family (SCO3201) that in condition of over-expression, strongly represses the strong antibiotic production and sporulation of S. coelicolor. Crystal structures of dimers of ligand-free SCO3201 obtained by scientists of the Universities of Greifswald (Germany) and Innsbruck (Austria) revealed that the DNA-binding domains of the dimer are held together in an unusually compact conformation and as a result, cannot span the distance between the two half-of its operator sites. Interestingly, the interaction of SCO3201 with its putative ligand, spermidine, coincides with a major structural rearrangement leading to an increased distance between the DNA-binding domains of the dimer that is predicted to allow its interaction with its operator sites. Consequently and in sharp contrast to what was observed for most TetR-like regulators, the binding of the ligand might facilitate, rather than abrogate, interaction of the regulator with its operator sites. Such ‘reverse’ induction mechanism, triggered by a nitrogen rich molecule, may explain the dramatic negative impact that over-expression of SCO3201 has on the ability of S. coelicolor to produce antibiotics and sporulate. The group MES characterized numerous potential targets of SCO3201 and the high promiscuity of this regulator was attributed to its long N terminal extension containing four positively charged residues (Arg28, 29, 34 and Lys30) that seem to be ideally positioned to stabilize SCO3201’s weak interaction with poorly related operator sites conferring to SCO3201 its relaxed specificity.

More information: here

Contact: Marie-Joëlle Virolle <marie-joelle.virolle@i2bc.paris-saclay.fr>

The cyclic dinucleotide c-di-AMP is a mediator of osmotic stress and bile salt resistance with a role in host colonization in the opportunistic pathogen Clostridioides difficile.

To colonize the host and cause disease, the human enteropathogen Clostridioides difficile must sense, respond,
and adapt to the harsh environment of the gastrointestinal tract. We showed that the production and
degradation of cyclic diadenosine monophosphate (c-di-AMP) were necessary during different phases of
C. difficile growth, environmental adaptation, and infection. The production of this nucleotide second messenger
was essential for growth because it controlled the uptake of potassium and also contributed to biofilm
formation and cell wall homeostasis, whereas its degradation was required for osmotolerance and resistance
to detergents and bile salts. The c-di-AMP binding transcription factor BusR repressed the expression of genes
encoding the compatible solute transporter BusAA-AB. Compared with the parental strain, a mutant lacking
BusR was more resistant to hyperosmotic and bile salt stresses, whereas a mutant lacking BusAA was more
susceptible. A short exposure of C. difficile cells to bile salts decreased intracellular c-di-AMP concentrations,
suggesting that changes in membrane properties induce alterations in the intracellular c-di-AMP concentration.
A C. difficile strain that could not degrade c-di-AMP failed to persist in a mouse gut colonization model as
long as the wild-type strain did. Thus, the production and degradation of c-di-AMP in C. difficile have pleiotropic
effects, including the control of osmolyte uptake to confer osmotolerance and bile salt resistance, and
its degradation is important for host colonization.

More information here

Contact: Johann Peltier <johann.peltier@i2bc.paris-saclay.fr>

We demonstrated that a deficit in ATP leads to the activation of the expression of biosynthetic pathways directing the biosynthesis of a certain type of antibiotics in Streptomyces lividans, a strain in which these pathways are usually silent.

In most Streptomyces species, antibiotic production is triggered in a condition of phosphate limitation, a condition that is known to be correlated with a low intracellular ATP content compared to growth in a condition of phosphate proficiency. This observation suggests that a low ATP content might be a direct trigger of antibiotic biosynthesis. In order to test this hypothesis, we introduced into the model strain Streptomyces lividans, a functional and a non-functional ATPase cloned into the replicative vector pOSV206 and expressed under the control of the strong ErmE* promoter. The functional ATPase was constituted by the α (AtpA), β (AtpB) and γ (AtpD) sub-units of the native F1 part of the ATP synthase of Streptomyces lividans that, when separated from the membrane-bound F0 part, bears an ATPase activity. The non-functional ATPase was a mutated version of the latter, bearing a 12 amino acids deletion encompassing the active site of the AtpD sub-unit. S. lividans was chosen to test our hypothesis since this strain hardly produces any antibiotics. However, it possesses the same biosynthetic pathways of various specialized metabolites as Streptomyces coelicolor, a phylogenetically closely related strain that produces these metabolites in abundance. Our results demonstrated that the over-expression of the functional ATPase, but not that of its mutated version, indeed correlated with the production of the bioactive metabolites of the CDA, RED and ACT clusters. These results confirmed the long known and still mysterious link existing between a phosphate limitation leading to an ATP deficit and the triggering of antibiotic biosynthesis. Based on this work and on previous published results of our group, we propose an entirely novel conception of the nature of this link.

More information here

Contact: Marie-Joëlle Virolle <marie-joelle.virolle@i2bc.paris-saclay.fr

The first inhibitors of the undecaprenyl-pyrophosphate phosphatase BacA, showing BacA-targeted antibacterial activity, were discovered by high-troughput virtual screening, molecular dynamics and biological activity measurements.

The peptidoglycan is an essential heteropolymer of the bacterial envelope that guarantees the integrity and the shape of all bacterial cells. This is also their Achilles’s heel as underlined by the extent of compounds that impede its structure or biogenesis. The biosynthesis of peptidoglycan relies on a lipid carrier, the undecaprenyl phosphate, which is used as a cargo for the export of the subunits across the plasma membrane. As a byproduct of peptidoglycan polymerization, the lipid carrier is released in the undecaprenyl pyrophosphate form, which must be recycled. To this end, it undergoes a dephosphorylation catalyzed by the membrane enzyme BacA, which is specific and highly conserved in bacteria. In the present study, we identified the first small antibacterial compounds displaying inhibitory activity towards BacA using high-throughput virtual screening (HTVS). We prepared a virtual library of 8 million commercial compounds, followed by HTVS through molecular docking using the 3D structure of BacA, that we recently resolved (El Ghachi et al., Nat Commun, 2018), and molecular dynamics snapshots to account for the flexibility of the protein. Of 83 best compounds computationally selected, one hit compound inhibited BacA activity in vitro. Subsequently, an additional 33 scaffold analogs were selected, of which 6 compounds exhibited BacA inhibition. The half-maximal inhibitory concentration (IC50) values of these compounds ranged from 42 to 366 μM. Importantly, the best compounds also displayed an antibacterial activity against Escherichia coli that was further demonstrated to be dependent on BacA. This overall strategy and the identified structural scaffold of these inhibitors provide a solid foundation for the further development of potent BacA-targeted inhibitors and the design of novel antibiotics.

More information: https://www.sciencedirect.com/science/article/pii/S2001037022001660?via%3Dihub

Contact: Thierry Touzé <thierry.touze@i2bc.paris-saclay.fr>

A proteomic study indicated that the ability of the pptA/sco4144 mutant strain of S. lividans to produce antibiotics is linked to a deficit in the generation of NADP(H) leading to high oxidative stress, a powerful trigger of a specific class of antibiotics.

Streptomyces coelicolor and Streptomyces lividans, are closely related strains possessing the same biosynthetic clusters directing the biosynthesis of various specialized bio-active metabolites including that of the blue polyketide, actinorhoddin (ACT), that bears anti-oxidant properties. However most of these pathways are expressed in S. coelicolor but not in S. lividans. Interestingly, the disruption of a single gene (pptA) of S. lividans conferred to this strain the ability to produce ACT. A comparative quantitative proteomic analysis of these strains was carried out in order to define the potentially common features of the ACT producing strains. The abundance of proteins of numerous pathways differed greatly between S. coelicolor and the S. lividans strains, especially those of central carbon metabolism and respiration. S. coelicolor is characterized by a weak glycolytic activity resulting into a low carbon flux through the Pentose Phosphate Pathway, involved in the generation of NADPH, a co-factor of thioredoxin reductases necessary to combat oxidative stress. Furthermore, the complex I of the respiratory chain thought to generate reactive oxygen/nitrogen species was highly abundant in S. coelicolor. Oxidative stress was thus predicted to be high in S. coelicolor. In contrast, the S. lividans strains had rather similar proteins abundance for most pathways except for that involved into NAD(P)(H) metabolism. PptA being an accessory protein forcing polyphosphate into a conformation allowing their efficient use by various enzymes taking polyphosphate as a donor of phosphate and energy, including the ATP/Polyphosphate-dependent NAD kinase SCO1781, this suggested that the phosphorylation of NAD into NADP, would be inefficient in the pptA mutant resulting in low NADP(H) levels and thus high oxidative stress. Our results thus indicated that high oxidative stress is the common feature triggering ACT biosynthesis in S. coelicolor and in the pptA mutant of S. lividans.

More information: https://www.frontiersin.org/articles/10.3389/fmicb.2021.813993/full

contact: Marie-Joëlle VIROLLE <marie-joelle.virolle@i2bc.paris-saclay.fr>

The diverse metabolic pathways and biologically induced mineralization mechanisms employed by Thermococcales would thus help them to survive in a broad range of extreme environments characterized by the high temperatures and high iron and sulfide contents.

Thermococcales, a major order of archaea inhabiting the iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, have been shown to rapidly produce abundant quantities of pyrite FeS2 in iron–sulfur-rich fluids at 85°C, suggesting that they may contribute to the formation of ‘low temperature’ FeS2 in their ecosystem. We show that this process operates in Thermococcus kodakarensis only when zero-valent sulfur is directly available as intracellular sulfur vesicles. Whether in the presence or absence of zero-valent sulfur, significant amounts of Fe3S4 greigite nanocrystals are formed extracellularly. We also show that mineralization of iron sulfides induces massive cell mortality but that concomitantly with the formation of greigite and/or pyrite, a new generation of cells can grow. This phenomenon is observed for Fe concentrations of 5 mM but not higher suggesting that above a threshold in the iron pulse all cells are lysed. We hypothesize that iron sulfides precipitation on former cell materials might induce the release of nutrients in the mineralization medium further used by a fraction of surviving non-mineralized cells allowing production of new alive cells. This suggests that biologically induced mineralization of iron-sulfides could be part of a survival strategy employed by Thermococcales to cope with mineralizing high-temperature hydrothermal environments.

More information: https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/1462-2920.15915

Contact: Aurore Gorlas  <aurore.gorlas@i2bc.paris-saclay.fr>

Cell cycle regulating GANTC methylation patterns in the Sinorhizobium meliloti genome are remodelled during differentiation of this endosymbiont within plant cells, suggesting an epigenetic regulation of a bacterial differentiation process.

In the rhizobium-legume symbiosis, the symbiotic bacteria are housed inside specific plant cells of root nodules where they fix nitrogen. These endosymbiotic rhizobia, called bacteroids, are metabolically differentiated and adapted to intracellular life. In legumes belonging to the genus Medicago, bacteroid differentiation of the symbiont Sinorhizobium meliloti involves also irreversible cellular modifications, including cell enlargement and genome amplification. By genome-wide DNA methylation analysis with SMRT-seq during the different stages of bacteroid differentiation in wild type plants as well as in a panel of plant mutants whose nodules contain endosymbionts blocked at various stages of differentiation, we obtained in this study evidence of dysregulated GANTC methylation patterns during bacteroid differentiation. We therefore propose that epigenetic control by the DNA methylase CcrM is a driving factor for the endoreduplication of the differentiated bacteroids.

More information: https://doi.org/10.1128/mSystems.01092-21

Contact person: Peter Mergaert 

Team Plant-Bacteria Interactions

We show that DNA supercoiling can be flipped from positive to negative in the archeon Thermococcus kodakarensis without adverse effect for its growth. This archaeon seems to be remarkably resistant to such topological stress, in stark contrast to bacteria in which DNA supercoiling is tightly regulated by topoisomerases.

In all cells, DNA topoisomerases dynamically regulate DNA supercoiling allowing essential DNA processes such as transcription and replication to occur. How this complex system emerged in the course of evolution is poorly understood. Intriguingly, a single horizontal gene transfer event led to the successful establishment of bacterial gyrase in Archaea, but its emergent function remains a mystery. To better understand the challenges associated with the establishment of pervasive negative supercoiling activity, we expressed the gyrase of the bacterium Thermotoga maritima in a naïve archaeon Thermococcus kodakarensis which naturally has positively supercoiled DNA. We found that the gyrase was catalytically active in T. kodakarensis leading to strong negative supercoiling of plasmid DNA which was stably maintained over at least eighty generations. An increased sensitivity of gyrase-expressing T. kodakarensis to ciprofloxacin suggested that gyrase also modulated chromosomal topology. Accordingly, global transcriptome analyses revealed large scale gene expression deregulation and identified a subset of genes responding to the negative supercoiling activity of gyrase. Surprisingly, the artificially introduced dominant negative supercoiling activity did not have a measurable effect on T. kodakarensis growth rate. Our data suggest that gyrase can become established in Thermococcales archaea without critically interfering with DNA transaction processes.

More information here.

Contact person: Tamara Basta

The transcriptional regulation of the biosynthesis and resistance to netropsin is not only controlled by a transcriptional regulator, Cgc1, but also by netropsin itself, which induces the expression of the resistance genes and of cgc1 by a new type of feedforward induction mechanism.

Understanding the mechanisms of regulation of specialized metabolite production can have important implications both at the level of specialized metabolism study (expression of silent gene clusters) and at the biotechnological level (increase of the production of a metabolite of interest). We report here the first study on the regulation of the biosynthesis of a metabolite from the pyrrolamide family, congocidine (netropsin). Most pyrrolamides bind into the minor groove of DNA, specifically in A/T-rich regions, which gives them numerous biological activities, such as antimicrobial and antitumoral activities. We demonstrate that Cgc1, a cluster-situated, atypical orphan response regulator, controls congocidine biosynthesis and resistance. In addition, we show that congocidine induces the expression of the operon containing the resistance genes, offering protection against congocidine to cells that are not yet producing it. Finally, our results reveal that congocidine induces its own biosynthesis through the induction of the transcription of cgc1, in a new type of feed-forward induction mechanism.

More information here.

Contact person: Sylvie Lautru