Publications
2024
Split Reporters Facilitate Monitoring of Gene Expression and Peptide Production in Linear Cell-Free Transcription-Translation Systems
Levrier A, Capin J, Mayonove P, Karpathakis II, Voyvodic P, DeVisch A, Zuniga A, Cohen-Gonsaud M, Cabantous S, Noireaux V, Bonnet J, ACS Synth Biol, 2024
@TOME 3.0: Interfacing Protein Structure Modeling and Ligand Docking
Pons JL, Reys V, Grand F, Moreau V, Gracy J, Exner TE, Labesse G, J Mol Biol, 2024
LactoSpanks: A Collection of IPTG Inducible Promoters for the Commensal Lactic Acid Bacteria Lactobacillus gasseri
Fristot E, Cambray G, Bonnet J, ACS Synth Biol, 2024
2023
SecretoMyc, a web-based database on mycobacteria secreted proteins and structure-based homology identification using bio-informatics tools
Gracy J, Vallejos-Sanchez K, Cohen-Gonsaud M, Tuberculosis (Edinb), 2023
A Mycobacterium tuberculosis Effector Targets Mitochondrion, Controls Energy Metabolism, and Limits Cytochrome cExit
Martin M, deVisch A, Boudehen YM, Barthe P, Gutierrez C, Turapov O, Aydogan T, Heriaud L, Gracy J, Neyrolles O, Mukamolova GV, Letourneur F, Cohen-Gonsaud M, Microbiol Spectr, 2023
An optimized electrotransformation protocol for Lactobacillus jensenii
Fristot E, Bessede T, Camacho Rufino M, Mayonove P, Chang HJ, Zuniga A, Michon AL, Godreuil S, Bonnet J, Cambray G, PLoS One, 2023
2022
Computational Methods for the Design of Recombinase Logic Circuits with Adaptable Circuit Specifications
Zuniga A, Bonnet J, Guiziou S, Methods Mol Biol, 2022
A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples
Zfaniga A, Munoz-Guamuro G, Boivineau L, Mayonove P, Conejero I, Pageaux GP, Altwegg R, Bonnet J, Front Bioeng Biotechnol, 2022
A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples
Zuniga A, Munoz-Guamuro G, Boivineau L, Mayonove P, Conejero I, Pageaux GP, Altwegg R, Bonnet J, Front Bioeng Biotechnol, 2022
Evaluating and mitigating clinical samples matrix effects on TX-TL cell-free performance
Voyvodic PL, Conejero I, Mesmoudi K, Renard E, Courtet P, Cattoni DI, Bonnet J, Sci Rep, 2022
Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates
Sabeti Azad M, Cardoso Batista A, Faulon JL, Beisel CL, Bonnet J, Kushwaha M, J Vis Exp, 2022
PeroxiHUB: A Modular Cell-Free Biosensing Platform Using H2O2as Signal Integrator
Soudier P, Zuniga A, Duigou T, Voyvodic PL, Bazi-Kabbaj K, Kushwaha M, Vendrell JA, Solassol J, Bonnet J, Faulon JL, ACS Synth Biol, 2022
Cryo-EM structure of transcription termination factor Rho from Mycobacterium tuberculosis reveals bicyclomycin resistance mechanism
Saridakis E, Vishwakarma R, Lai-Kee-Him J, Martin K, Simon I, Cohen-Gonsaud M, Coste F, Bron P, Margeat E, Boudvillain M, Commun Biol, 2022
Differentially Optimized Cell-Free Buffer Enables Robust Expression from Unprotected Linear DNA in Exonuclease-Deficient Extracts
Batista AC, Levrier A, Soudier P, Voyvodic PL, Achmedov T, Reif-Trauttmansdorff T, DeVisch A, Cohen-Gonsaud M, Faulon JL, Beisel CL, Bonnet J, Kushwaha M, ACS Synth Biol, 2022
2021
Engineered l-Lactate Responding Promoter System Operating in Glucose-Rich and Anoxic Environments
Zuniga A, Camacho M, Chang HJ, Fristot E, Mayonove P, Hani EH, Bonnet J, ACS Synth Biol, 2021
Programmable receptors enable bacterial biosensors to detect pathological biomarkers in clinical samples
Chang HJ, Zuniga A, Conejero I, Voyvodic PL, Gracy J, Fajardo-Ruiz E, Cohen-Gonsaud M, Cambray G, Pageaux GP, Meszaros M, Meunier L, Bonnet J, Nat Commun, 2021
The study of the determinants controlling Arpp19 phosphatase-inhibitory activity reveals an Arpp19/PP2A-B55 feedback loop
Labbe JC, Vigneron S, Mechali F, Robert P, Roque S, Genoud C, Goguet-Rubio P, Barthe P, Labesse G, Cohen-Gonsaud M, Castro A, Lorca T, Nat Commun, 2021
Computational Methods for the Design of Recombinase Logic Circuits
Guiziou S, Bonnet J, Methods Mol Biol, 2021
2020
Rational programming of history-dependent logic in cellular populations
Zuniga A, Guiziou S, Mayonove P, Meriem ZB, Camacho M, Moreau V, Ciandrini L, Hersen P, Bonnet J, Nat Commun, 2020
Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M
Cardozo Gizzi AM, Espinola SM, Gurgo J, Houbron C, Fiche JB, Cattoni DI, Nollmann M, Nat Protoc, 2020
TADs or no TADS: lessons from single-cell imaging visualization of chromosome architecture
Cardozo Gizzi AM, Cattoni DI, Nollmann M, J Mol Biol, 2020
Synthetic receptors to understand and control cellular functions
Chang HJ, Bonnet J, Meth Enzymol, 2020
2019
Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112
Alqaseer K, Turapov O, Barthe P, Jagatia H, De Visch A, Roumestand C, Wegrzyn M, Bartek IL, Voskuil MI, O'Hare HM, Ajuh P, Bottrill AR, Witney AA, Cohen-Gonsaud M, Waddell SJ, Mukamolova GV, Mol Microbiol, 2019
Metabolic perceptrons for neural computing in biological systems
Pandi A, Koch M, Voyvodic PL, Soudier P, Bonnet J, Kushwaha M, Faulon JL, Nat Commun, 2019
PEPOP 2.0: new approaches to mimic non-continuous epitopes
Demolombe V, de Brevern AG, Felicori L, NGuyen C, Machado de Avila RA, Valera L, Jardin-Watelet B, Lavigne G, Lebreton A, Molina F, Moreau V, BMC Bioinformatics, 2019
Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors
Voyvodic PL, Pandi A, Koch M, Conejero I, Valjent E, Courtet P, Renard E, Faulon JL, Bonnet J, Nat Commun, 2019
Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms
Cardozo Gizzi AM, Cattoni DI, Fiche JB, Espinola SM, Gurgo J, Messina O, Houbron C, Ogiyama Y, Papadopoulos GL, Cavalli G, Lagha M, Nollmann M, Mol Cell, 2019
Structural basis for chemically-induced homodimerization of a single domain antibody
Lesne J, Chang HJ, De Visch A, Paloni M, Barthe P, Guichou JF, Mayonove P, Barducci A, Labesse G, Bonnet J, Cohen-Gonsaud M, Sci Rep, 2019
Hierarchical composition of reliable recombinase logic devices
Guiziou S, Mayonove P, Bonnet J, Nat Commun, 2019
Benchmarking the PEPOP methods for mimicking discontinuous epitopes
Demolombe V, de Brevern AG, Molina F, Lavigne G, Granier C, Moreau V, BMC Bioinformatics, 2019
2018
Two Faces of CwlM, an Essential PknB Substrate, in Mycobacterium tuberculosis
Turapov O, Forti F, Kadhim B, Ghisotti D, Sassine J, Straatman-Iwanowska A, Bottrill AR, Moynihan PJ, Wallis R, Barthe P, Cohen-Gonsaud M, Ajuh P, Vollmer W, Mukamolova GV, Cell Rep, 2018
An engineered device for indoleacetic acid production under quorum sensing signals enables Cupriavidus pinatubonensis JMP134 to stimulate plant growth
Zuniga A, De la Fuente F, Federici F, Lionne C, Bonnet J, de Lorenzo V, Gonzalez B, ACS Synth Biol, 2018
An automated design framework for multicellular recombinase logic
Guiziou S, Ulliana F, Moreau V, Leclere M, Bonnet J, ACS Synth Biol, 2018
Sequence-dependent catalytic regulation of the SpoIIIE motor activity ensures directionality of DNA translocation
Chara O, Borges A, Milhiet PE, Nollmann M, Cattoni DI, Sci Rep, 2018
TADs are 3D structural units of higher-order chromosome organization in
Szabo Q, Jost D, Chang JM, Cattoni DI, Papadopoulos GL, Bonev B, Sexton T, Gurgo J, Jacquier C, Nollmann M, Bantignies F, Cavalli G, Sci Adv, 2018
Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia
Bonneau M, Atyame C, Beji M, Justy F, Cohen-Gonsaud M, Sicard M, Weill M, Nat Commun, 2018
A modular receptor platform to expand the sensing repertoire of bacteria
Chang HJ, Mayonove P, Zavala A, De Visch A, Minard P, Cohen-Gonsaud M, Jerome B, ACS Synth Biol, 2018
DNA Organization and Superesolved Segregation
Cattoni DI, Fiche JB, Le Gall A, Nollmann M, Methods Mol Biol, 2018
2017
Disulfide driven folding for a conditionally disordered protein
Fraga H, Pujols J, Gil-Garcia M, Roque A, Bernardo-Seisdedos G, Santambrogio C, Bech-Serra JJ, Canals F, Bernado P, Grandori R, Millet O, Ventura S, Sci Rep, 2017
Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions
Cattoni DI, Gizzi AMC, Georgieva M, Di Stefano M, Valeri A, Chamousset D, Houbron C, Dejardin S, Fiche JB, Gonzalez I, Chang JM, Sexton T, Marti-Renom MA, Bantignies F, Cavalli G, Nollmann M, Nat Commun, 2017
Microbially derived biosensors for diagnosis, monitoring and epidemiology
Chang HJ, Voyvodic PL, Zuniga A, Bonnet J, Microb Biotechnol, 2017
Identification of B and T cell epitope based peptide vaccine from IGF-1 receptor in breast cancer
Mahdavi M, Moreau V, Kheirollahi M, J Mol Graph Model, 2017
Biological Fate of Fe3O4 Core-Shell Mesoporous Silica Nanoparticles Depending on Particle Surface Chemistry
Rascol E, Daurat M, Da Silva A, Maynadier M, Dorandeu C, Charnay C, Garcia M, Lai-Kee-Him J, Bron P, Auffan M, Liu W, Angeletti B, Devoisselle JM, Guari Y, Gary-Bobo M, Chopineau J, Nanomaterials (Basel), 2017
LppM impact on the colonization of macrophages by Mycobacterium tuberculosis
Deboosere N, Iantomasi R, Queval CJ, Song OR, Deloison G, Jouny S, Debrie AS, Chamaillard M, Nigou J, Cohen-Gonsaud M, Locht C, Brodin P, Veyron-Churlet R, Cell Microbiol, 2017
Imaging of Bacterial Chromosome Organization by 3D Super-Resolution Microscopy
Le Gall A, Cattoni DI, Nollmann M, Methods Mol Biol, 2017
2016
Phosphorylation-mediated regulation of the Staphylococcus aureus secreted tyrosine phosphatase PtpA
Brelle S, Baronian G, Huc-Brandt S, Zaki LG, Cohen-Gonsaud M, Bischoff M, Molle V, Biochem Biophys Res Commun, 2016
Mycobacterium tuberculosis LppM Displays an Original Structure and Domain Composition Linked to a Dual Localization
Barthe P, Veyron-Churlet R, de Visch A, Gilleron M, Saliou JM, Tomavo S, Nigou J, Brodin P, Cohen-Gonsaud M, Structure, 2016
A part toolbox to tune genetic expression in Bacillus subtilis
Guiziou S, Sauveplane V, Chang HJ, Clerte C, Declerck N, Jules M, Bonnet J, Nucleic Acids Res, 2016
Bacterial partition complexes segregate within the volume of the nucleoid
Le Gall A, Cattoni DI, Guilhas B, Mathieu-Demaziere C, Oudjedi L, Fiche JB, Rech J, Abrahamsson S, Murray H, Bouet JY, Nollmann M, Nat Commun, 2016
Nanometer resolved single-molecule colocalization of nuclear factors by two-color super resolution microscopy imaging
Georgieva M, Cattoni DI, Fiche JB, Mutin T, Chamousset D, Nollmann M, Methods, 2016
Analytic framework for a stochastic binary biological switch
Innocentini GC, Guiziou S, Bonnet J, Radulescu O, Phys Rev E, 2016
Synthesis, decoration, and cellular effects of magnetic mesoporous silica nanoparticles
Nyalosaso JL, Rascol E, Pisani C, Dorandeu C, Dumail X, Maynadier M, Gary-Bobo M, Lai-Kee-Him J, Bron P, Garcia M, Devoisselle JM, Prat O, Guari Y, Charnaya C, Chopineau J, RSC Adv, 2016
2015
Cooperativity in Binding Processes: New Insights from Phenomenological Modeling
Cattoni DI, Chara O, Kaufman SB, Gonzalez Flecha FL, PLoS ONE, 2015
Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging
Marbouty M, Le Gall A, Cattoni DI, Cournac A, Koh A, Fiche JB, Mozziconacci J, Murray H, Koszul R, Nollmann M, Mol Cell, 2015
Stochastic Self-Assembly of ParB Proteins Builds the Bacterial DNA Segregation Apparatus
Sanchez A, Cattoni DI, Walter JC, Rech J, Parmeggiani A, Nollmann M, Bouet JY, Cell Syst, 2015
Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates
Courbet A, Endy D, Renard E, Molina F, Bonnet J, Sci Transl Med, 2015
The external PASTA domain of the essential serine/threonine protein kinase PknB regulates mycobacterial growth
Turapov O, Loraine J, Jenkins CH, Barthe P, McFeely D, Forti F, Ghisotti D, Hesek D, Lee M, Bottrill AR, Vollmer W, Mobashery S, Cohen-Gonsaud M, Mukamolova GV, Open Biol, 2015
The fluorescence properties and binding mechanism of SYTOX green, a bright, low photo-damage DNA intercalating agent
Thakur S, Cattoni DI, Nollmann M, Eur Biophys J, 2015
A matter of scale: how emerging technologies are redefining our view of chromosome architecture
Cattoni DI, Valeri A, Le Gall A, Nollmann M, Trends Genet, 2015
Phosphorylation of Mycobacterium tuberculosis ParB Participates in Regulating the ParABS Chromosome Segregation System
Baronian G, Ginda K, Berry L, Cohen-Gonsaud M, Zakrzewska-Czerwinska J, Jakimowicz D, Molle V, PLoS ONE, 2015
2014
Kinetics of bioaccumulation of heavy metals in Odontesthes bonariensis is explained by a single and common mechanism
Blanco MV, Cattoni DI, Carriquiriborde P, Grigera JR, Chara O, Ecological Modelling, 2014
A novel mode of regulation of the Staphylococcus aureus Vancomycin-resistance-associated response regulator VraR mediated by Stk1 protein phosphorylation
Canova MJ, Baronian G, Brelle S, Cohen-Gonsaud M, Bischoff M, Molle V, Biochem Biophys Res Commun, 2014
Chromosome organization: original condensins
Cattoni DI, Le Gall A, Nollmann M, Curr Biol, 2014
The RpfC (Rv1884) atomic structure shows high structural conservation within the resuscitation-promoting factor catalytic domain
Chauviac FX, Robertson G, Quay DH, Bagneris C, Dumas C, Henderson B, Ward J, Keep NH, Cohen-Gonsaud M, Acta Crystallogr F Struct Biol Commun, 2014
Antimicrobial treatment improves mycobacterial survival in nonpermissive growth conditions
Turapov O, Waddell SJ, Burke B, Glenn S, Sarybaeva AA, Tudo G, Labesse G, Young DI, Young M, Andrew PW, Butcher PD, Cohen-Gonsaud M, Mukamolova GV, Antimicrob Agents Chemother, 2014
Oleoyl-Coenzyme A Regulates Interaction of Transcriptional Regulator RaaS (Rv1219c) with DNA in Mycobacteria
Turapov O, Waddell SJ, Burke B, Glenn S, Sarybaeva AA, Tudo G, Labesse G, Young DI, Young M, Andrew PW, Butcher PD, Cohen-Gonsaud M, Mukamolova GV, J Biol Chem, 2014
Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome
Vogelmann J, Le Gall A, Dejardin S, Allemand F, Gamot A, Labesse G, Cuvier O, Negre N, Cohen-Gonsaud M, Margeat E, Nollmann M, PLoS Genet, 2014
2013
Super-resolution imaging of bacteria in a microfluidics device
Cattoni DI, Fiche JB, Valeri A, Mignot T, Nollmann M, PLoS ONE, 2013
The RYMV-encoded viral suppressor of RNA silencing P1 is a zinc-binding protein with redox-dependent flexibility
Gillet FX, Cattoni DI, Petiot-Becard S, Delalande F, Poignavent V, Brizard JP, Bessin Y, Dorsselaer AV, Declerck N, Sanglier-Cianferani S, Brugidou C, Vignols F, J Mol Biol, 2013
Recruitment, assembly, and molecular architecture of the SpoIIIE DNA pump revealed by superresolution microscopy
Fiche JB, Cattoni DI, Diekmann N, Langerak JM, Clerte C, Royer CA, Margeat E, Doan T, Nollmann M, PLoS Biol, 2013
Equivalence between Euler angle conventions for the description of tensorial interactions in liquid NMR: application to different software programs
Dosset P, Barthe P, Cohen-Gonsaud M, Roumestand C, Demene H, J Biomol NMR, 2013
Mycobacterium tuberculosis S-adenosyl-l-homocysteine hydrolase is negatively regulated by Ser/Thr phosphorylation
Corrales RM, Leiba J, Cohen-Gonsaud M, Molle V, Kremer L, Biochem Biophys Res Commun, 2013
Structure and DNA-binding properties of the Bacillus subtilis SpoIIIE DNA translocase revealed by single-molecule and electron microscopies
Cattoni DI, Thakur S, Godefroy C, Le Gall A, Lai-Kee-Him J, Milhiet PE, Bron P, Nollmann M, Nucleic Acids Res, 2013
SpoIIIE mechanism of directional translocation involves target search coupled to sequence-dependent motor stimulation
Cattoni DI, Chara O, Godefroy C, Margeat E, Trigueros S, Milhiet PE, Nollmann M, EMBO Rep, 2013
Mechanisms of interaction between Candida albicans and Streptococcus mutans: an experimental and mathematical modelling study
Brusca MI, Irastorza RM, Cattoni DI, Ozu M, Chara O, Acta Odontol Scand, 2013
2012
Single-molecule super-resolution imaging in bacteria.
Cattoni DI, Fiche JB, Nollmann M, Curr. Opin. Microbiol., 2012
A two-stage model for lipid modulation of the activity of integral membrane proteins
Dodes Traian MM, Cattoni DI, Levi V, Gonzalez Flecha FL, PLoS One, 2012
A novel mode of regulation of the Staphylococcus aureus catabolite control protein A (CcpA) mediated by Stk1 protein phosphorylation.
Leiba J, Hartmann T, Cluzel ME, Cohen-Gonsaud M, Delolme F, Bischoff M, Molle V, J. Biol. Chem., 2012
The C-terminal domain of the virulence factor MgtC is a divergent ACT domain.
Yang Y, Labesse G, Carrere-Kremer S, Esteves K, Kremer L, Cohen-Gonsaud M, Blanc-Potard AB, J. Bacteriol., 2012
2011
2010
The structure of PknB extracellular PASTA domain from mycobacterium tuberculosis suggests a ligand-dependent kinase activation
Barthe P, Mukamolova GV, Roumestand C, Cohen-Gonsaud M, Structure, 2010
Phosphorylation of the Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein reductase MabA regulates mycolic acid biosynthesis
Veyron-Churlet R, Zanella-Cleon I, Cohen-Gonsaud M, Molle V, Kremer L, J Biol Chem, 2010
2009
Dynamic and structural characterization of a bacterial FHA protein reveals a new autoinhibition mechanism
Barthe P, Roumestand C, Canova MJ, Kremer L, Hurard C, Molle V, Cohen-Gonsaud M, Structure, 2009
The Mycobacterium tuberculosis Ser/Thr kinase substrate Rv2175c is a DNA-binding protein regulated by phosphorylation
Cohen-Gonsaud M, Barthe P, Canova MJ, Stagier-Simon C, Kremer L, Roumestand C, Molle V, J Biol Chem, 2009
2008
2007
2006
Bacterial resuscitation factors: revival of viable but non-culturable bacteria
Keep NH, Ward JM, Robertson G, Cohen-Gonsaud M, Henderson B, Cell Mol Life Sci, 2006
Wake up! Peptidoglycan lysis and bacterial non-growth states
Keep NH, Ward JM, Cohen-Gonsaud M, Henderson B, Trends Microbiol, 2006
2005
The structure of a resuscitation-promoting factor domain from Mycobacterium tuberculosis shows homology to lysozymes
Cohen-Gonsaud M, Barthe P, Bagneris C, Henderson B, Ward J, Roumestand C, Keep NH, Nat Struct Mol Biol, 2005
Ligand-induced fit in mycobacterial MabA: the sequence-specific C-terminus locks the conformational change
Cohen-Gonsaud M, Ducasse-Cabanot S, Quemard A, Labesse G, Proteins, 2005
2004
Design of an amphipatic a-helical hairpin peptide
Barthe P, Cohen-Gonsaud M, Aldrian-Herrada G, Chavanieu A, Labesse G, Roumestand C, Comptes Rendus Chimie, 2004
(1)H, (15)N, and (13)C chemical shift assignments of the resuscitation promoting factor domain of Rv1009 from Mycobacterium tuberculosis
Cohen-Gonsaud M, Barthe P, Pommier F, Harris R, Driscoll PC, Keep NH, Roumestand C, J Biomol NMR, 2004
From molecular modelling to drug design
Cohen-Gonsaud M, Catherinot V, Labesse G, Douguet D, Nucleid Acids and Molecular Biology, Vol 15, Practical Bioinformatics, Ed. by J.M. Bujnicki (2004) Springer-Verlag, 2004
Resuscitation-promoting factors possess a lysozyme-like domain
Cohen-Gonsaud M, Keep NH, Davies AP, Ward J, Henderson B, Labesse G, Trends in Biochemical Sciences, 2004
In vitro inhibition of the Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein reductase MabA by isoniazid
Ducasse-Cabanot S, Cohen-Gonsaud M, Marrakchi H, Nguyen M, Zerbib D, Bernadou J, Daffe M, Labesse G, Quemard A, Antimicrob Agents Chemother, 2004
Heptahelical domain of metabotropic glutamate receptor 5 behaves like rhodopsin-like receptors
Goudet C, Gaven F, Kniazeff J, Vol C, Liu J, Cohen-Gonsaud M, Acher F, Prezeau L, Pin JP, Proc Natl Acad Sci U S A, 2004