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Adress: UMR FARE, 2 esplanade Roland-Garros, BP 224, 51686 Reims, France
Phone: +33 (0)3 26 77 36 25
Fax: +33 (0)3 26 77 35 99
Email: gabriel.paes@inrae.fr

Research Topics

In the context of the bioeconomy and the rational use of bioresources, the biotechnological processes for converting lignocellulosic biomass (which forms the skeleton of plants) are still too inefficient. The aim of my research project is therefore to develop original approaches to gain a better understanding of the architecture of plant walls (secondary walls), with the aim of modelling these walls in 3D and highlighting and then ranking the chemical and physical markers that block their controlled destructuration, a phenomenon known as recalcitrance. The strategy consists of characterising these cell walls at different spatial scales, in particular by analysing their accessibility by measuring the mobility and interactions of chemical or biological fluorescent probes (antibodies, enzymes or CBMs) in controlled model systems and native and pretreated wall systems, using confocal microscopy (FRAP, FRET) and 4D imaging techniques. The data set obtained is then correlated with the chemical, physical and spectral properties of the lignocellulosic systems and their propensity to be saccharified. This strategy, applied to contrasting samples (species, tissues, pre-treatment), highlights the markers limiting saccharification and suggests solutions for mitigating them.

Key-words

Biorefinery, lignocellulosic biomass, recalcitrance, enzyme, accessibility, interaction, microscopy, fluorescence, 4D, modelling

Projects

France 2030 funding: coordinator of the FillingGaps project (2023-2027), participants in the GalaxyBioProd (2023-2027) and Amaretto (2023-2027) projects

ANR funding: participant in the LABEL project (2023-2025), participant in the BIOMOD project (2019-2022), leader of the Lignoprog project (2015-2018), task leader for the Funlock project (2014-2017)

Funding by Carnot 3BCAR: participant in the Ecodrop project (2023-2024)

Funding from INRAE / INRA: participant in the FluoFlax4D (2018-2019) and Apsali (2013-2014) projects, task leader for the Mobiprot project (2013-2014), participant in the Enzydam project (2011-2012)

Funding from the Grand Est Region: participant in the HyCGreen project (2018-2022), several PhD theses funded

BPI: participant in the Futurol project (2009-2018)

Synchrotron SOLEIL: several projects on the DISCO, SMIS and PSYCHE lines

Career

Since 2021 - Lab Director, FARE laboratory (Reims)

Since 2017 - Research Director (DR2), FARE laboratory

2014-2017 - Researcher (CR1), FARE laboratory

2009-2014 - Junior Researcher (CR2), FARE laboratory

2007-2009 - Research Engineer, METabolic EXplorer, Clermont-Ferrand - Development of enzymatic assays and of purification and characterization protocols of enzymes dedicated to metabolic engineering projects to produce chemicals by industrial fermentation

2006-2007 - Post-doctoral Researcher, University of Marseille / INRA (UMR 1163 BCF) - Integration of genes coding for new cellulases and hemicellulases into the genome of Trichoderma reesei

2005-2006 - Post-doctoral Researcher, University of Nantes / CNRS (UMR 6204 U3B) and University of Reims / INRA (UMR 614 FARE) -  Structure/function relationships between the motion of hemicellulases loops and substrate accessibility by coupling molecular modelling and robotics approaches

Education

2016 - Accreditation to supervise research (Habilitation à Diriger des Recherches), University of Reims Champagne-Ardenne. Exploring Lignocellulosic Biomass!

2001-2005 - PhD in Biochemistry and Molecular Biology, University of Reims Champagne-Ardenne / INRA (UMR FARE) - Structure/function study of thermostable hemicellulases: GH-11 xylanase and GH-51 arabinofuranosidase from Thermobacillus xylanilyticus

2004 - Marie-Curie fellow (during my PhD), The Danish University of Pharmaceutical Sciences, Copenhague (Danemark) - Cristallisation and X-ray cristallography of hemicellulases

2001 - Master of Physical-chemistry and quality of bio-products, Sciences Faculty, University of Nantes

2000 - Master of Chemistry-Biology, IUP of Chemistry-Biology, University of Nantes

Skills

Design and characterization of bio-inspired lignocellulosic assemblies
Design and characterization of fluorescent probes
Characterization of plant biomass samples
Microscopy tools to investigate cell wall architecture (fluorescence spectroscopy, FLIM), probe mobility (FRAP) and interactions (FLIM-FRET)
3D & 4D imaging
Molecular biology of procaryotes and microbiology of procaryotes/eukaryotes
Purification and biochemical/enzymatic/biophysical characterization of recombinant proteins/enzymes
Cristallogenesis, molecular modelling/dynamics of proteins

Publications

43 peer-reviewed articles, 100+ oral communications and posters in national and international meetings, 5 book chapters

Selected relevant articles (15):

du Pasquier J, Paës G*, Perré P* (2023) Principal factors affecting the yield of dilute acid pretreatment of lignocellulosic biomass: A critical review. Bioresource Technol. 369, 128439. https://doi.org/10.1016/j.biortech.2022.128439

Leroy A, Devaux M-F, Fanuel M, Chauvet H, Durand S, Alvarado C, Habrant A, Sandt C, Rogniaux H, Paës G*, Guillon F* (2022) Real-time imaging of enzymatic degradation of pretreated maize internodes reveals different cell types have different profiles. Bioresource Technol. 353, 127140. https://doi.org/10.1016/j.biortech.2022.127140

Escamez S, Terryn C, Gandla ML, Yassin Z, Scheepers G, Näsholm T, Sundman O, Jönsson LJ, Lundberg-Felten J, Tuominen H, Niittylä T, Paës G (2021) Fluorescence Lifetime Imaging as an In Situ and Label-Free Readout for the Chemical Composition of Lignin. ACS Sus. Chem. Eng. 9, 17381-17392. http://doi.org/10.1021/acssuschemeng.1c06780

Bourlieu C, Astruc T, Barbe S, Berrin J-G, Bonnin E, Boutrou R, Hugouvieux V, Le Feunteun S, Paës G* (2020) Enzymes to unravel bioproducts architecture. Biotechnol. Adv. 41, 107546. http://doi.org/10.1016/j.biotechadv.2020.107546

Zoghlami A, Paës G* (2019) Lignocellulosic biomass: understanding recalcitrance and predicting hydrolysis. Front. Chem. 7. Open Access

Zoghlami A, Refahi Y, Terryn C, Paës G* (2019) Multimodal characterization of acid-pretreated poplar reveals spectral and structural parameters strongly correlate with saccharification. Bioresour. Technol. 293, 122015. DOI

Herbaut M, Zoghlami A, Habrant A, Falourd X, Foucat L, Chabbert B, Paës G (2018) Multimodal analysis of pretreated biomass species highlights generic markers of lignocellulose recalcitrance. Biotech. Biofuels 11, 52. Open Access

Terryn C, Paës G, Spriet C (2018) FRET-SLiM on native autofluorescence: a fast and reliable method to study interactions between fluorescent probes and lignin in plant cell wall. Plant Methods 14, 74. Open Access

Chabbert B, Habrant A, Herbaut M, Foulon L, Aguié-Béghin V, Garajova S, Grisel S, Bennati-Granier C, Gimbert-Herpoel I, Jamme F, Refregiers M, Sandt C, Berrin JG, Paës G (2017) Action of lytic polysaccharide monooxygenase on plant tissue is governed by cellular type. Scientific Reports 7, 17792. Open Access

Auxenfans T, Terryn C, Paës G (2017) Seeing biomass recalcitrance through fluorescence. Scientific Reports 7, 8838. Open access

Auxenfans T, Crônier D, Chabbert B, Paës G (2017) Understanding the structural and chemical changes of plant biomass following steam explosion pretreatment. Biotechnology for Biofuels 10, 36. Open Access

Paës G, Habrant A, Ossemond J, Chabbert B (2017) Exploring accessibility of pretreated poplar cell walls by measuring dynamics of fluorescent probes. Biotechnology for Biofuels 10: 15 Open Access

Fong M, Berrin JG, Paës G (2016) Investigation of the binding properties of a multi-modular GH45 cellulase using bioinspired model assemblies. Biotechnology for Biofuels 9: 12 Open access

Paës G (2014) Fluorescent probes for exploring plant cell wall deconstruction: a review. Molecules 19: 9380-9402 Open access

Paës G, Burr S, Saab MB, Molinari M, Aguié-Béghin V and Chabbert B (2013) Modeling progression of fluorescent probes in bioinspired lignocellulosic assemblies. Biomacromolecules 14: 2196–2205 DOI

Paës G, Berrin JG, Beaugrand J (2012) GH11 xylanases: structure/function/properties relationships and applications. Biotechnol. Adv. 30: 564-592 DOI

PhD supervision

Solmaz HOSSEIN KHANI (2022-2025). Spatio-temporal modelling of the deconstruction of lignocellulosic biomass. Thesis director, co-supervisor: Yassin Refahi (FARE)

Edwige AUDIBERT (2022-2025). Structure-property relationships of wood pre-treated by continuous steam stripping. CIFRE thesis with the Société Européenne de Biomasse. Thesis director, co-director: Caroline Rémond (FARE)

Julien DU PASQUIER (2021-2024). Multi-scale modelling of steam explosion pretreatment of lignocellulosic biomass. Thesis director, co-director: Patrick Perré (CentraleSupélec Biotechnology Chair)

Laurent CHAPILLON (2020-2023). Modélisation spatio temporelle de la déconstruction de la biomasse lignocellulosique. Thesis director, co-supervisor: Yassin Refahi (FARE)

Amandine LEROY (2018-2022). Approche multi-échelle du suivi dynamique de la déconstruction de la biomasse lignocellulosique. Thesis director, co-director: Fabienne Guillon (INRAE)

Aya ZOGHLAMI (2016-2019). Techniques avancées de microscopie pour l’imagerie 4D de la déconstruction de la biomasse lignocellulosique. Thesis director, co-director: Christine Terryn (Université de Reims Champagne-Ardenne) and Yassin Refahi (FARE). Thesis defended on December 12t, 2019 (3 articles)

Eléonore LAMBERT (2015-2018). Apports de la Microscopie à Force Atomique à l’étude de phénomènes dynamiques en biologie et développement instrumental associé. Thesis director: Michaël Molinari (Université de Reims Champagne-Ardenne). Supervisor of a thesis chapter. Thesis defended on December 20th, 2018 (2 articles)

Mickaël HERBAUT (2014-2017). Déconstruction de la biomasse lignocellulosique : corrélation entre la progression et l’activité enzymatiques. Directeur de thèse. Thesis defended on October 13th, 2017 (5 articles)

Expertise

Expert for Horizon Europe programme (12 projects reviewed in 2019 and 2020)

Member of the Editorial Board of Frontiers in Chemistry (Frontiers, since 2019)

Associate Editor of Biotechnology for Biofuels and Bioproducts (BMC, since 2023)

Guest Editors of Special Issues:

- From Biomass to Advanced Bio-Based Chemicals & Materials: A Multidisciplinary Perspective, in Frontiers in Chemistry (2019)

- Pretreatment of lignocellulosic biomass: established technologies and recent developments, in JoVE (2020)

- Lignocellulose: Properties, Characterization and Applications, in Polysaccharides (2021)

- Lignocellulosic Polymers: Fractionation and Characterization, in Polymers (2021)

- Biomass Steam Explosion Pretreatment for Bioproducts, in Frontiers in Chemistry (2021)

- Understanding Plant Cell Wall Recalcitrance for Efficient Lignocellulose Processing, in Frontiers in Chemistry (2022)

Reviewer: 110+ articles and reviews in 30+ different journals

Other Activities

FARE lab: responsible for the Communication.

Transform Division at INRAE: coordinator of the "Design of the food and bioproducts quality" challenge (2017-2020), elected member of the Scientific Board (2016-2020), member of the Specialised Scientific Commission (CSS) SIAMM for the evaluation of researchers, member of the Communication group (2014-)

National: member of the French Plant Cell Wall network (since 2014), CFDT trade union member (2011-2014 & 2015-2017) at the INRA National Commission for Researchers.

International: chairman of the Exploring Lignocellulosic Biomass (ELB) meeting held in Reims in 2016, 2018, member of the management committee of the COST "Waste biorefinery technologies for accelerating sustainable energy processes" (2021-2025), one of the two representatives for France.