Section des Unités de recherche

Evaluation report Research unit :

Laboratoire d'Enzymologie et Biochimie structurales

CNRS

March 2009

Section des Unités de recherche

Evaluation report Research unit :

Laboratoire d’Enzymologie et Biochimie structurales

CNRS

March 2009

Evaluation report

The research unit :

Name of the research unit : Laboratoire d'Enzymologie et Biochimie structurales (LEBS)

Requested label : UPR CNRS

N° in case of renewal : UPR3082

Head of the research unit : Jacqueline CHERFILS

Research organization :

CNRS

Other university or school :

University Paris 11

Dates of the visit :

December 2-3, 2008

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Members of the visiting committee

Chairman of the commitee : M. Vincent VILLERET, University of Lille 1 and 2

Other committee members : Mme Emmanuelle CARON, Imperial College London, UK

M. Stephen CUSACK, University of Grenoble

M. Mario GIMONA, University of Salzburg

Ms. Anne HOUDUSSE, UNiversity of Paris 5

M. Ludger JOHANNES, University of Paris 11

M. David PIGNOL, University of Aix-Marseille 2

M. Human REZAEI, JUniversity of Paris 6

M. Philippe BENAS, University of Paris 5

CNU, CoNRS, CSS INSERM, représentant INRA, INRIA, IRD…..) representatives : Mme Laurence SERRE, CoNRS representative

Observers

AERES scientific representative : M. Thierry RABILLOUD

University or school representative : M. Jacques BITTOUN, University Paris 11

Research organization representative : M. Thierry MEINNEL, CNRS

Evaluation report

1• Short presentation of the research unit — Numbers of lab members : 68 including

o researchers with teaching duties : 2 o full time researchers : 21 o postdoctoral fellows : 16 o PhD students : 17 o engineers, technicians and administrative assistants : 12

— Numbers of HDR : 16

— Numbers of PhD students who have obtained their PhD : 12

— Average lenght of a PhD during the past 4 years : 3.5 years

— Numbers of PhD students with fellowships : 17

— Numbers of lab members with a PEDR : 0

— Numbers of “publishing” lab members (among permanent researchers with or without teaching duties): 23

2 • Preparation and execution of the visit The schedule of the visit was prepared through emails and phone calls between the lab director, the AERES representative and the evaluation committee chairman, taking into account directives transmitted by the AERES. The on-site evaluation was also prepared by emails between the committee members.

The visit started at 11h00 on December 2, 2008 and ended at 18h30 on December 3, 2008. General features of the unit were first presented by the director. This presentation introduced, in an historical perspective, the current themes of research in the lab, and emphasized the importance of multidisciplinary approaches as part of the general strategy to study proteins and their interactions. General aspects of current and proposed management practices were presented. Also, the technical facility of the LEBS, launched in 2006, was introduced and situated in the context of the future structural biology pole which is developed within the IMAGIF project of the Gif campus. These general presentations by the director were followed by presentations by each Principal Investigator (PI) of the different research groups and also by the head of the technical facility. All but one were in english. The committee discussed briefly with each PI immediately after the presentation. Ample time was available for discussions with the groups in the context of poster sessions where all members of each group were present. Lunch was taken with the group heads. The committee visited the infrastructures at the end of the first evaluation day. The committe also had discussions with the representatives from the CNRS and University of Paris 11, and separately with representatives of the technical and administrative staff, students, post-docs and researchers. The visit took place in very good conditions, thanks to the efficient local organisation under the supervision of the lab director. The committee was entirely happy with the way the evaluation was prepared and conducted.

3 • Overall appreciation of the activity of the research unit, of its links with local, national and international partners This unit was created in January 2008 and is evaluated by this visiting committee for its anticipated renewal, in order to be in phase with the next contractual "Plan Quadriennal" of the University Paris 11. Since its creation the unit has performed very well, allowing the emergence of new projects that reinforces its thematic coherence around two federating themes: the study of complex protein assemblies and the study of the molecular bases of pathologies, with applications to the discovery of compounds with therapeutic potential. The committee perceived the dynamism of the scientific management inspired by the director. Two new emerging groups have been created since 2006. The group "Molecular recognition of intracellular trafficking", rewarded by a prestigious "chaire d'excellence ANR" 2007, and the group "Complex assemblies and morphogenesis", which shed new light and strengthen cellular biochemical studies

4

already going on in the unit. Two groups have reoriented their research following the retirement of their previous heads, with one of them ("tRNA modification enzymes") created as a 2 years team. Finally, five well established groups complement the research flowchart of the unit.

Another strong point of the unit is the vast expertise found in biochemistry, structural and cellular biology, and also the development of interfaces between physics, biology and chemistry. Support must be given to ensure that this expertise is maintained in the future. Also, the increasing request for crystallographic expertise, both within the unit and in its scientific neighborhood at Gif and at the University of Paris 11 would justify the arrival of a new group experienced in macromolecular crystallography. The committee supports the wish of the director to welcome such a new group. This is necessary to keep the current crystallography experts of the unit focused on their main research projects.

A technical facility has been launched in 2006, aiming at a centralization of facilities in cloning, biochemistry, biophysical and structural analyses. This facility is under the responsibility of a research engineer. Since 2007 this platform is opened to external users coming from teams of the Gif campus and also from the synchrotron SOLEIL, and it has partially integrated the IMAGIF platform of the campus. The committee supports the platform development, which is required for a unit of this size. So far all the technical expertise for the development, maintenance and running have been provided by technicians coming from research groups and by researchers, which represents an impoverishment of the technical support within the research teams, and an extra load on researchers. Appropriate resources should be provided in the forthcoming years to further reinforce technical support of both the research teams and the facilities. This will be important to consider in the light of the future restructuring of the Gif campus and further involvement of the unit in the IMAGIF initiative.

An indicator of the unit’s activity is the publication output: 98 articles since 2006, with an excellent quality as revealed by the impact factors of the journals: e.g. Mol Cell, PNAS, EMBO J., J. Biol. Chem, Nature,.... More than fifty crystallographic structures of proteins and complexes have been reported. International visibility is illustrated by many prestigious conferences organized by the unit, among them two EMBO courses, one FASEB Summer Research Conference co-sponsored by the CNRS, and one Jacques Monod Conference. International recognition is also clear from the number of invited lectures (49).

The unit is also active in teaching and training activities. Seven theses have been defended during the 2006-2008 period, and each group has currently at least one PhD student. Twenty-six post-docs have worked in the unit during this period. 60% are foreigners, a ratio that underlines the international opening of the unit. Most of the researchers of the unit are involved in teaching activities, and the current contractual period ("contrat quadriennal") has been the opportunity for them to propose a new Master module. The unit is also in charge of the administration of students of the "proteins" pole of the doctoral school of the University Paris 11. In the light of the strong involvement of the unit in teaching activities, the committee pointed out that support from the University to the unit should be reinforced: only one professor from the university Paris 11 is developing her research activities in the unit, and there is a lack of "enseignants-chercheurs" within the unit.

Overall, the unit appears to be an internationally competitive unit. The committee congratulates the director for her successful work in increasing synergies between groups, attracting new very promising leaders, and developing the international competitiveness of the unit. Appropriate support should be provided in the forthcoming years to maintain and further stimulate its development.

4 • Specific appreciation team by team and/or project by project Group "Cytoskeleton Dynamics and Motility"

This group has a long standing interest in understanding the molecular and physical parameters which underly the force producing mechanisms that drive cell movement by regulated actin polymerization. These processes are relevant for a broad variety of physiological and pathophysiological processes including embryonic development, cell transmigration and tissue repair, tumor cell invasion and metastasis, immune response, synapse plasticity, and the uptake and propagation of bacterial and viral pathogens. Over the past years the laboratory has led the international research in the field of biochemical control of actin polymers, and the self-assembly by a variety of accessory and regulatory proteins. The reconstituted in vitro system developed in the laboratory led to the first definition of the minimal motile machinery in cells. The research capitalizes on the combinatorial exploitation of expertise at the interface of biology, physics, and chemistry. The current and future research directions remain at the leading edge of

5

international research in this field and have a high potential to contribute further important knowledge to the understanding of cell motility via cytoskeleton dynamics. The proposal to carry on the definition of sub-modular entities of the actin machinery (e.g. focusing on the constitutive co-filament forming tropomyosin family) is good. The group will also address a currently rapidly expanding and important field, namely that of mechanosensation and mechanotransduction via the cytoskeleton. The group has the proper awareness of the modular schemes in protein and interaction network construction. In summary the future strategies capitalize realistically on the available knowledge and expertise, as well as on the available instruments and resources.

The group is very productive and consistently publishes original research papers in high impact Journals (Cell, Molecular Cell, Nature Cell Biology PNAS, JBC, EMBO J). This fact is even more significant as the lab has a small/medium size compared to other internationally competitive laboratories. The group undertakes collaborations both within the unit and with outside research groups, but in most cases has the lead in the research projects. The work of the group has had significant impact on the field of actin dynamics and cell motility, and benchmarked biochemical in vitro reconstitution systems. Training of students and post docs in the lab has a demonstrated effect on the future career perspectives, and has generated a cohort of excellently trained researchers with wide perspectives for a future employment in research and industry at the European and wider international level.

The group forms a coherent unit with considerable expertise being present in biochemistry, structural biology, biophysics, and cell biology. The biophysics unit that is attached to the team is excellent. However, the committee noticed that many potential synergies with new and existing groups at unit were not well exploited, and encourages the PI to develop more synergies within the unit. Considering the unique expertise and international standing of this research group the committee encourages the group members to contribute as much as possible to national and international training activities (albeit the extensive travel schedule of the team leader identifies considerable training-trough-presentation activities). Team members should be more strongly encouraged to participate in and present at international conferences to increase their international visibility and hence their future career perspectives. The Team is well funded and supported from a number of grants acquired from national and international sources (including HFSP and EMBO). It is unclear, however, why the team is not applying for more EC support - in particular schemes of the Marie Curie program (e.g. ITN) would help recruit early stage researcher to the group and fill the training gap. The group should be a welcome participant in larger (multinational and multi-site) research proposals such as those being called under the Health scheme in FP7 of the European Commission.

The committee congratulates this group for its outstanding scientific activity and prompts the institutions to give full support for the coming years until the retirement of the PI, in order to ensure adequate exploitation of the results generated over the next three years. In light of the foreseeable retirement of the PI the committee identified the need for the unit director to engage at the earliest possible time in constructive discussions on the future development and structure of this group. Potential candidates with the capacity to continue this important work and lead a group of scientists should be identified (from within or outside the group if appropriate), and required promotion/recruitment strategies should be developed for these individuals.

DYNAMIQUE DU CYTOSQUELETTE ET MOTILITÉ

Note de l’équipe

Qualité scientifique et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

A+

A+

A+

A+

A+

Group "Small GTP-binding proteins: structure, interactions and cellular regulations"

This dynamic group is actually directed by 2 PIs (1 DR1 and 1 DR2) and comprises 2 CR1, 1 associated researcher from ANR, 1 technician, and 2 PhD. Four post-doctoral fellows also worked in the group from 2006 to 2008. In the next contractual plan, the group will be headed by the DR1, due to the retirement of the DR2. The group focuses on small GTP-binding proteins (GTPases) and combine methods of structural, biochemical and cellular biology to investigate GTPase-controlled processes from the molecule to the function in cells. The research focuses on the Arf and Rho/Rac families. 1) This group has done pioneering and outstanding research in the field of guanine nucleotide exchange factors (GEFs) inhibitors, with the characterization of a first inhibitor of a GEF, brefeldin A. This work leads to a

6

novel concept for this inhibition of protein-protein interactions, termed interfacial inhibition. This concept has been extended and allowed the discovery of a novel inhibitor of Arf activation, LM11, directed against the Arf1/ARNO complex. 2) A second theme of research concerned the study of large ArfGEFs involved in Golgi traffic with the identification of domain-domain interactions in GBF1 and BIGs, analysis of the auto-inhibition process, and structure determination of the Sec7 domain of human BIG1. Finally, the third theme of research concerned the cellular studies of RhoGDIs, with the identification of Sec3, a component of the exocyst trafficking complex as a partner of RhoGDI3 N-terminal domain, the functional analysis of RhoGDI3, RhoG and Sec3 cooperation in MDCK cells, and the analysis of RhoGDI3 and RhoG colocalization in dynamic vesicule-like compartments.

The group plans to build on its internationally recognized expertise in GEFs inhibitors, to tackle the discovery of such inhibitors of therapeutic interest in the field of cancer (Arf6/Arf6GEFs), hypertension (RhoA/p115RhoGEF), infection (Arf and bacterial GEFs) and inflammation (NADPH oxidase). Many of these studies will benefit from established or novel collaborations with members of a national consortium on GEFs inhibitors wich has been created by the PI of the group. This is an obvious development considering the outstanding expertise and leadership of the group in this field. A second theme of research will focus on Arf and membranes, with the aim to understand the autoinhibition and mechanism of activation of a bacterial ArfGEF, and the biophysical analysis of RabFIPs as membrane tethers in cytokinesis. Also, in collaboration with the group "Molecular recognition of intracellular trafficking", they will study the mechanism of Rab and Arf GTPases crosstalk that program the transformation of a Rab membrane into an Arf membrane to mediate vesicular trafficking steps. Finally, two emerging projects will be initiated, in Rho signaling in NADPH oxidase activation (work supported by the Arthritis foundation), and in the structural biology of hedgehog signaling complexes. The group has an excellent publication record, with 21 publications since 2005. It has also been very active in training, with two PhD theses defended in 2008, and 3 PhD students currently in the lab. This group has been very successful in raising funds, with support from ANR, HFSP, Arthritis Foundation, ARC, Cancéropôle, Marie-Curie,...

The committee has appreciated the quality of the presentation, as well as the outstanding scientific results and future projects. It has also greatly appreciated the synergy that is emerging with another group, for instance with the "Molecular recognition of intracellular trafficking" group. An important event is the departure of 4 permanent members of the group by 2010. Two members, the IE and one CR1, recently retired in 2008, and the DR2 will retire in the end of 2009. In addition, the group technician is also leaving, as a result of a promotion on external competition. Consequently the group will be considerably reduced by 2010 and will lose a strong expertise in cellular biology. For this reason the RhoDGI3 project will be completed and published within the next two years and left over to cell biologists outside the team. The committee strongly recommends to give support to this group in order to maintain its international excellence, via the recruitment of an expert structural biochemist and/or a cellular biochemist. This group has also an immediate need for ITA support.

PETITES PROTÉINES G: STRUCTURES, RÉGULATIONS ET INTERACTIONS CELLULAIRES

Note de l’équipe

Qualité scientifique et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

A+

A+

A+

A+

A+

Group "Complex assemblies and morphogenesis"

This young group, composed of one researcher and one PhD student, joined the unit at the beginning of 2008, and thus will be fully assessed at the next cycle of evaluation. The group focuses on the biochemical and cellular analysis of multiprotein complexes relevant to actin dynamics and morphogenesis. One example of these complexes is the WAVE complex, which controls the formation of Arp2/3—dependent lamellipodium extension downstream of Rac. The dynamics and regulation of such stoechiometric multiprotein complexes are particularly challenging to study in the context of whole cells, making the understanding of their regulation all the more difficult to decipher.

The group has developed astute methodologies to attack the cutting-edge question of how the WAVE complex is regulated. These approaches, based on reconstitution of knock-out cells with electroporated proteins, are and will be capitalized upon in the future. They can indeed be transposed to identify and study other multiprotein complexes,

7

either in the team (which is already working on an exciting new complex), in the unit or through collaborations, some of which are already in place. Importantly, the group has embraced the unit philosophy of mutualism, with plans for streamlining and making accessible their technologies for the study of multiprotein complexes on a service-basis in the context of IMAGIF. Other aspects of the proposed project include further biochemical and cellular characterization of the mechanisms regulating multiprotein complex assembly and function. The research plan is very interesting, carefully thought through and presents the perfect mix of focus and exploration, ambition and realism. Importantly, whenever needed, internal or external collaborations are in place.

The team’s scientific production is excellent for a group this size, with five publications in the past four years in very competitive journals (eg PNAS, J Cell Biol, PLOS one). This includes three publications signed as first or last author by the group leader. The recent arrival of an additional PhD student and a post-doc will help maintain and most probably further improve these records. The group is already well-funded, with grants from the CNRS, ANR and FRM success. Finally, the group leader is contributing significantly to post-graduate teaching and formation, through the organization of national and international courses on cytoskeletal dynamics.

The committee supports this very promising group, with excellent scientific focus and a very good balance of activities overall. Already very well integrated at the unit it is a clear asset to the laboratory and it should be supported to further develop its full potential. Extensive collaborations with other groups of the unit should be developed, and the committee expects the well established groups of the unit to collaborate. The most immediate need of this group is ITA support, to absorb the growing demands, for example in terms of protein production and analysis. ASSEMBLAGES COMPLEXES ET MORPHOGÉNÈSE

Note de l’équipe

Qualité scientifique

et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

A

A

A

Non noté

A+

Group "tRNA modification enzymes: mechanistic and structural studies"

This small group (1CR1 with HDR, 1IR, 1doc and 1 post-doc) was created as a 2 years team in 2007. It originated historically from the "enzymologie de l'ARN" group, whose PI retired recently. The group focuses on S-Adenosylmethionine-dependant methyl-transferases (MTases) involved in the chemical modifications of tRNA. The publication record appears satisfactorily. Out of the 13 articles published by members of this group in the last 2 years, 6 are related to historical activities on Glucosamine-6P synthase and 7 papers concern the structural and functional characterization of various tRNA modifying enzymes. Since no structure of RNA/enzyme complexes was obtained, a strategy has been initiated to trap covalent RNA-enzyme complexes for co-crystallization experiments. The scientific activity of the group is supported by funds from ARC and ANR-PCV.

The committee had mixed feelings about this group. Although the group is undoubtedly competent in its field and quite productive, the committee is concerned about the means available to provide an international visibility given the scientific context of the unit. The committee is concerned that this small group appears thematically isolated from the rest of the scientific topics developed in the current unit. In addition, most of the structural studies carried out on MTases were mostly initiated before the birth of the group. Attention should be paid in the future to the development of real original cutting-edge projects in order to obtain notoriety on these topics and a long-term viability of the team. In such context, the functional and structural characterization of flavin-dependent RNA methyl-transferases appears as a promising project. The recommendation of the committee is to initiate a reflection between the director of the unit and the PI in order to find out the best possible scientific context to develop this research, or to identify a thematic convergence fostering internal collaborations within the unit.

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ENZYMES DE MODIFICATION DES TRNAS: ÉTUDES MÉCANISTIQUES ET STRUCTURALES

Note de l’équipe

Qualité scientifique et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

B

A

B

B

C

Group "Molecular recognition of intracellular trafficking"

The PI has joined the UNIT on October 23, 2006. The group is composed of 2 staff scientists (DR2 and CR1), 1 temporary engineer (CDD AI), 2 PhD students and 1 post-doctoral fellow. This group has been granted a prestigious "Chaire d'excellence" of the ANR in 2007. It has made groundbreaking contributions by identifying guanine nucleotide exchange factors as a target of the small fungal metabolite brefeldin A, thereby contributing in a major way to a research domain that is today actively pursued by many laboratories in the world and that has become a hot spot of membrane biology research. Capitalizing on these important contributions, the group is now extending its studies of ArfGEFs. One project is based on the original recent observation that rather than being solely regulatory elements, ArfGEFs directly interact with effector proteins. This exciting observation has major consequences for the current model of the reaction cascade by which Arf proteins regulate membrane traffic. The group will follow up on this conceptual challenge through molecular dissection of the newly discovered interactions and by studying functional consequences. Another challenging project exploits the team's recent finding that one of the interacting partners of the ArfGEF GBF1 is the lipid droplet protein ATGL. Current experimental evidence from the group strongly suggests that GBF1 is a key component to a pathway leading to the biogenesis of one type of droplets in cells. The studies that are proposed are expected to make major contributions in this important field of research.

The group also explores the function of ArfGEFs in viral biogenesis and has already demonstrated a role for GBF1 in the production of poliovirus. Apart from their obvious importance for a fundamental understanding of how viruses exploit the endomembrane system, these studies also offer new insights into possible intervention strategies.

Finally, the group is exploring, in collaboration with a leading group in France, the cell biology of GMAP210, a Golgi tethering factor for which the collaborators could recently suggest an elegant scheme of curvature-mediated association cascades. This long-lasting and ongoing collaboration should enable the group to extend its studies to model membrane systems that would be of high added value to the conceptual explorations that are proposed in its different projects.

This group has published in high-visibility journals (Nature, Cell, Dev Cell, NCB …), and despite her recent arrival from the US to France, the PI has started producing again. The PI is regularly invited to speak at international conferences (including FEBS, FASEB, ASCB meetings). The committee was very pleased by the excellence of the presentation, the results and future plans of this group. The recommendation of the committee is to continue this brilliant start with the same motivation, and develop successfully the promising collaborations with teams within the unit. This will undoubtedly reinforce and strengthen the visibility of the UNIT in this field at the international level. The committee recommends giving full support to this young and dynamic group.

RECONAISSANCE MOLÉCULAIRE DU TRAFIC INTRACELLULAIRE

Note de l’équipe

Qualité scientifique et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

A+

A+

A+

A+

A+

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Group "Structural cellular biochemistry : tubulin and the control of microtubule assembly"

This group is composed of two staff scientists, 1 DR1 (PI) and 1 CR1, and 4 students. It focuses its activity on questions related to the regulation of microtubule assembly. Microtubules (MTs) are essential dynamic constituents of the cytoskeleton involved in such fundamental cell functions as cell division, intracellular traffic or neuronal growth. Assembly dynamics of MTs is a regulated process in the cell that involves a number of proteins such as stathmin, a tubulin sequestering protein. Several pharmacological compounds also intervene with the dynamics of MTs and are currently used in cancer therapy. Combining physical chemistry, biochemistry and structural biology, the team has characterized conditions to describe the structure of two tubulin heterodimers bound to a stathmin fragment. This structure has provided a number of insights that help understand the differences between straight and curved assembly of tubulin dimers and the structural basis important for nucleotide exchange and GTP hydrolysis. This tool has also been used to describe at ~4Å resolution the binding site of several compounds of pharmacological interest in collaboration with pharmaceutical companies.

The group has international expertise on the structure of tubulin and has already contributed to several significant papers. It has published eight papers in the past four years. Four are original research papers related to this project (Nature 2005, Biochemistry 2005, Biochemistry 2007, EMBO Rep. 2008). The group leader also contributed to two reviews not directly related to MTs and a review/methodological paper was published in Methods Mol Med 2007. A few publications have been delayed due to industrial embargo. The expertise of the group is recognized in the microtubule field and in the cancer drug industry. The fundamental questions addressed to understand how the GTP hydrolysis cycle contributes to the MT assembly is interesting since it is at the base of the dynamic instability of microtubules, a critical property of this cytoskeleton component essential for cell division. To gain insights about the structural basis of this property, new peptides of MT binding proteins will be used to address new questions. This elegant approach is however artificial and it is unclear how much insights can be extracted from these sequestered tubulin dimer complexes to better understand in vivo polymerisation of microtubules.

The team currently addresses critical questions concerning microtubule assembly. The approach that uses small intrinsically disordered proteins to stabilize tubulin dimers is innovative and risky. One of the weaknesses of the approach so far has been the resolution of the structures solved, which prevents description of the interactions at atomic detail.

Several structural approaches will be pursued in parallel to obtain a structural description of the tubulin state that is competent for polymerization. Members of the team are involved in the further strategic development of the project and the group leader also develops interesting intellectual discussions with the Cytoskeleton dynamics group, also at the UNIT, who had intensely contributed to the MT system but now focuses on actin, another cytoskeleton polymer. A few international collaborations are set up whenever they can add to the project. The team is funded with industrial contracts and supports from the ARC and Ligue associations. Two ANR grants are finishing in December 2008.

The committee has appreciated the quality of the presentation, as well as of the scientific results and future projects. In this regard, the committee encourages the group members to participate more often to international conferences to increase their international visibility.

BIOCHIMIE CELLULAIRE STRUCTURALE: TUBULINE ET CONTRÔLE DE L'ASSEMBLAGE DES MICTOTUBULES

Note de l’équipe

Qualité scientifique et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

A+

A+

A+

A+

A+

Group "Protein folding in vivo and conformational disease"

This group is composed of four staff scientists - 1DR2 (PI), 2 CR1, 1CR2, 2 ITAs (1 on a CDD contract), 2 post-doctoral fellows and 4 PhD students. This group is specialized in aggregation processes of Ure2 and Sup 35 proteins which are responsible for non mendelian information transmission in yeast. The main work of this dynamic group during the evaluated period can be declined as biochemical and structural characterization of the native state of Ure2 protein

10

and its aggregates forms. In this way the team has used a broad and impressive number of technical approaches to show that during the aggregation process of Ure2 its native structure is conserved. Theses results contrast with results reported in the literature on “infectious” Ure2 amyloidic fibrils. The domain implicated in this polymerization is not yet clearly defined and this question should be addressed in an early future by this dynamic and enthusiastic team.

In regard of the numerous publications of this group it is undoubtedly clear that they dominate the field of Ure2 and Sup 35 aggregations both in vitro and in vivo. However, the attempt to establish a parallelism between mammalian prion and yeast prion phenomenon did not fully convince the committee as it appeared that there was no relevance to make this relation, except in term of concept.

Concerning the proposed project, this group wants to explore the biological mechanisms of toxicity of mammalian amyloidic protein such as alfa-Synuclein and Abeta based on the experience accumulated on Ure2 and Sup35 aggregation in yeast and the role of chaperones in the aggregation. During the presentation, the PI did not detail the approaches foreseen to investigate such hot topic in this field. The committee feels that in this very competitive field the group has to find its niche as soon as possible.

The committee recognizes that this team has the potential to go deeper in the analysis of “prion like” phenomenon in yeast. Their previous experience on Ure2 aggregation in yeast and the role of chaperones in this aggregation will constitute a trump to extend their investigation to human amyloidosis.

REPLIEMENT DES PROTÉINES IN VIVO ET MALADIES CONFORMATIONNELLES

Note de l’équipe

Qualité scientifique et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

A

A

A

A

a

Group "Supramolecular assemblies in translation"

This group studies the particularities of aminoacyl-tRNA synthetases in higher eukaryotes, which compared to their prokaryotic counterparts often have additional appended domains at the N- or C-terminal. These domains mediate organization into higher order complexes, notably the multi-synthetase complex (MARS, 9 synthetases and 3 non-synthetase proteins) or confer non-canonical functions. The group applies a multi-disciplinary approach ranging from structural biology and enzymology/biochemistry to cell biology (Tap-tag, siRNA, confocual imaging, yeast 2-hybrid approaches) to studies at the organism level (genetic modification of C. elegans). The group has a high international reputation in the field, being one of only two groups (the other being in S. Korea) focusing on this important but challenging topic, which touches systems biology (e.g. compartmentalization of the protein synthesis machinery) and molecular medicine (apoptosis, cytokines, cancer and HIV infection). The PI is well known for doing very careful and rigorous work, based on a long experience in the field.

The current and future projects of the group are (1) Structural studies including crystallization trials, electron microscopy and small angle scattering of the MARS complex. The group has optimized rapid purification of MARS and is the best placed in the world to obtain detailed structural information. (2) studies in C. elegans, which is amenable to genetic modification, to understand the in vivo function of the appended domains of its synthetases as well as to understand the evolutionary origin and rationale of MARS. (3) Continued studies on the role of human lysyl-tRNA synthetase in packaging of tRNA3(lys) in HIV particles. The group has found that it is most likely the mitochondrial lysyl-tRNA synthetase that is specifically involved in this process and propose comprehensive studies to understand the molecular interactions involved (e.g. with Gag-Pol), the cellular pathways that enable mitochondrial lysyl-tRNA synthetase to be hijacked by HIV and screen for inhibitors of the interaction.

This group has a rather modest publication record both reflecting the challenging nature of the work and the relatively small size of the group. However the work of the group is of very high quality and is very positively evaluated and supported by the committee.

11

ASSEMBLAGES SUPRAMOLÉCULAIRES DANS LA TRADUCTION

Note de l’équipe

Qualité scientifique

et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

A

A

A

A

A

Group "Structural Signalling"

This team is composed by four staff scientists (2 PR2 and 2 CR1-CNRS), two technical assistants (1 IR2 and 1 AI sharing their working time with the UNIT technical platforms) and three PhD students. In the next contractual plan the current co-direction of the group will be replaced by a single headed direction. The committee approves the choice of the future PI of the group.

Members of this team have a strong expertise in crystallography. Their general interest is to decipher, by a structure/function approach, the molecular mechanisms of the regulation of transient protein complexes formed during the cellular signalling processes. In that context, these last two years, this team obtained interesting results on the regulation of the cellular signalling in bacteria and eukaryotes, that were published in international journals (10 papers published since January 2006 including 1 Plos Biology, 1 PNAS, 2 J Biol Chem, 3 Proteins). Although the activity of this team is driven by fundamental research, most of their structural studies have potential developments for human health as well. This group has investigated the molecular bases of the regulation mechanisms of Staphylococcus aureus tyrosine kinase CapB, which is related to the bacterial pathogenicity. Crystal structures of bacterial UMP kinase complexed to UMP, UTP and GTP provide the structural bases for developing new antibiotics. Finally, the structural studies of the poxviruses TMP kinase or Hsp90 chaperone are related to cancer research. The bacterial protein kinases (HprK/P and tyrosine kinases) and the complex Hsp90 chaperone machinery will be major structural projects developed in the coming years.

This group has so far been very successful in raising funds. Its activity is currently supported by a CNRS program “proteomics and protein engineering”, two ANR grants (ANR Microbiology-and-Immunology and ANR Young investigators) and an ARC grant. The co-supervision of students and co-signature by at least two seniors of papers published in high impact factor journals (2 J. Biol Chem, 1 Plos Biology) give evidence of an excellent synergy between the members of the team. This team has also a strong contribution to the UNIT scientific life, notably by its strong involvement in the organisation of internal seminars and by the responsibility of the technical staff and the involvement of senior scientists in supervising many technical platforms. This team has developed an excellent local collaborative network within the Paris region including a strong connexion with the local universities (Paris XI and Agro-Paris Tech) through teaching activities. Apart from the regional research collaborations, the current projects are also supported by several national collaborations. Nowadays, the team has few collaborations with international groups but this international aspect will be probably more developed in the coming years as the future projects include European collaborators.

The committee has appreciated the excellent research that has been accomplished in this group and the perspectives of future research plans. As experts in crystallography, this group is often contacted by others outside the UNIT to provide guidance on structure determination. The committee recommends focusing the work on the proposed proprietary research. Also, this group has been strongly invested in the setting-up and running of many technical platforms of the UNIT. In particular the research engineer of this group is now heading the UNIT technical facility. As a consequence, the technical support of this group is declining. The most immediate need of this group is ITA support.

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SIGNALISATION STRUCTURALE

Note de l’équipe

Qualité scientifique et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

A

A

A

A

A

5 • Appreciation of resources and of the life of the research unit Overall, the unit appeared well organised with good sharing of resources and the creation of a useful technical facility. The committee was pleased by all the efforts that have been undertaken over the last two years to improve the functioning of the unit. The unit has been equipped with a "Conseil de Laboratoire" and with all the appropriate tools (hygiène et sécurité ...) requested from regulatory aspects. The committee underlines the particular effort of the unit to maintain a good training level in various scientific and management fields, in particular for the technical staff. The unit does not only offer training to its members but also trains scientists from other places (one EMBO course and one INSERM-CNRS workshop).

Two safety officers and one person competent for radiation protection are in charge of these duties in the unit. In addition three members of the institute are in charge of chemical wastes and one of the biological wastes. All aspects linked to health and safety regulation are well managed and meet the expected requirements. In particular, all kind of risks (fire, explosions, radiations, laser as well as electrical, chemical and biological risks) are well identified and controlled. The committee highly appreciated the work done by the unit as a whole to meet all the required criteria.

Communication and animation strategies have been set up, as well as weekly seminars, both internal and external. A lab journal is frequently issued, a folder presenting the lab has been produced. A two-days laboratory retreat has been created, "les journées du UNIT", which will be organized every other year. Working groups are created whenever required, for the purchase of common equipment or the potential welcoming of new groups.

A clear strength of the unit over the past few years has been its ability to attract a number of energetic group leaders, and also to develop strong synergies between them and the existing research groups. The contribution of these groups to the unit is already excellent and highly promising for the future. Strong interactions are also developed with groups outside the UNIT on the Gif campus, for example with ICSN. The UNIT now has a strong non-francophone component with 60% of post-doctoral fellows coming from outside France, which is an indication of its dynamism and attractiveness.

Discussion with tenured staff, technical and administrative staff, postdoctoral and doctoral students was revealing. This indicated a large degree of cohesion and interaction between these groups and a general contentment in the way in which the unit functions. The representatives reported a general satisfaction about the conditions of work in the unit (training, space, access to conferences, good atmosphere) and the fact that they were consulted by the director on matters of concern. They were also satisfied that they had access to adequate additional lecture courses, both scientific and non-scientific and on career development issues. The unit is a member of the "Institut Fédératif de Recherches 115 Génomes: Structure, Fonction et Evolution" and is involved in the "Grand Campus Gif-Orsay" and actively participates, together with the University Paris XI, the CEA and the CNRS to the brainstorming about the future global organisation and scientific strategy in this area.

The unit has launched a technical facility, which is now fully operational. This facility should allow the UNIT to reinforce its expertise, acquire novel state-of-the-art equipment, and increase interactions between teams within and outside the lab. This equipment is already available in part to users of the campus and beyond, and will become available through the IMAGIF facility for both the academic and industrial communities. This will be actuated in part by the scheduled implementation of the cloning and crystallization facilities in the future IMAGIF building by 2011. Other resources will remain in the laboratory. The rooms currently accommodating these resources are very basic and not really appropriate. There are free rooms in the unit building that could be accommodated to receive these resources, providing sufficient funding is available from the institutions for their renovation.

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Finally, the unit anticipates to be part of a future "Pôle d'excellence et de formation en biologie structurale et protéomique". The committee has appreciated the strong involvement of the unit not only in the development of the Gif campus, but also for its active role in the future structuration of biological research in South Paris.

The committee observed that the development of the technical facility put some pressure on the research groups, and significantly contributed to an impoverishment of the technical support within the research groups. ITA support is required to maintain the expertise and competitiveness of the teams. So far, four teams of the unit do not have any ITA support at all.

6 •Recommendations and advice — Strong points :

High international visibility and world-wide leadership of some groups.

Ability to attract young talented group leaders.

Development of significant and high impact synergies between some research groups and in particular with new groups, allowing to focus and strengthen the unit on its main lines of research.

Significant success in attracting external funding at both the national and (to a lesser extent) international level.

Excellent combination of expertise in structural and cell biology, biochemistry, outstanding interdisciplinary approaches at the interfaces biology/physics and biology/chemistry

Excellent management and communication strategy.

— What needs to be improved :

ITA support is not adequate, neither for research groups nor for the technical facility.

Synergies between some groups with convergent research areas must be improved.

Inadequate scientific context for one group. A reflection must be initiated by the director to find out the best possible scientific context to develop its research.

Long term durability questioned for one group. A reflection with the current PI must be initiated by the director.

Marginal support from the University, despite the strong involvement of the unit in teaching and training.

— Recommendations :

The unit is productive, innovative and creative. The visiting committee was favourably impressed by the quality of the research and also by the quality of the governance. The committee highly recommends the renewal of the unit.

ITA support must be reinforced in the unit. It is crucial that the unit receives ITA support in the near future, to maintain the quality of the research and the development and running of the technical facility.

Inadequate scientific context for one group: a reflection must be initiated by the director to find out the best possible scientific context to develop its research.

Long term durability questioned for one group: a reflection with the current PI must be initiated by the director.

The committee warmly encourages the unit to continue to recruit new young promising group leaders.

Support from the University should be increased, in the light of the strong involvement of the unit in teaching and training.

Renovation of the unit building must be continued to optimally accommodate the technical facilities.

The expertise in crystallography should be reinforced to meet the demands from groups within or outside the unit.

The administrator of the unit will retire in 2009. Her replacement should be planned immediately.

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LABORATOIRE D'ENZYMOLOGIE ET BIOCHIMIE STRUCTURALES (UPR 3082

Note de l’unité

Qualité scientifique

et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

A+

A+

A+

A+

A+

15

Labora toi re d ’Enzy molog ie e t B ioch imie S tructu ra les

UPR 3082 C.N.R.S. - Bât. 34 - Avenue de la Terrasse - 91198 Gif-sur-Yvette Cedex, France

Tél : +33 (0)1 69 82 34 77 – Fax : +33 (0)1 69 82 31 29 - http://www.lebs.cnrs-gif.fr -

To the AERES

Comments on the AERES evaluation report on the UPR3082- LEBS

April 3, 2009

The director and the personnel of the LEBS wish to thank the president and the members of the AERES committee for their careful analysis, constructive recommendations and generous time investment. We are very pleased with the overall positive evaluation and will endeavour to implement its recommendations. Our responses regarding specific groups are presented below.

Sincerely,

Jacqueline Cherfils

Group tRNA-modification enzymes : mechanistic and structural studies The report does not appear to give a fair credit to the activity of this small group, which has done very well since it was created 2 years ago. Its activity is readily measurable: the group has published 13 articles, of which many are in high standard journals (4 JBC, 2 NAR, 2 JMB, 1 Curr. Op. Struct. Biol …), it has secured grants to support its research (ARC and ANR), and it has been successful in attracting and supervising PhD students and post-docs. We request therefore that the quality of the research is fully acknowledged on the basis of these objective figures, and is set apart from the question of whether the group should consider finding a more adequate environment for the visibility and expansion of its research themes. On the latter, the laboratory director and the PI agree to initiate a discussion on whether the research theme should be refocused to meet more closely the research directions of the LEBS, or a laboratory with a closer focus should be found. Group « Protein folding in vivo and conformational diseases » The group appreciates the overall positive evaluation of the committee. However, it feels that, given its long-standing expertise in the field, its adequate choice of collaborations and its high-profile funding for the project (FP7 and HFSP), the group is in a strong position to develop competitive research on its new theme on conformational diseases, rather than in a need to find a « niche ». The group also wants to emphasize that the relevance of yeast prion for understanding prion propagation in vertebrate is not merely « conceptual » as stated in the

Jacqueline Cherfils Directrice du Laboratoire Email : cherfils@lebs.cnrs-gif.fr Tel : 01 69 82 34 77

report, but is widely accepted as demonstrated by no less than 80 reviews on the topic during the last decade. Group « Structural cellular biochemistry : tubulin and the control of microtubule assembly » The group appreciates the overall positive evaluation of the committee but wishes to respond to the concern expressed in the report that the structural analysis of the sequestered tubulin dimer might not be relevant to microtubule polymerization in vivo. The group emphazises that this is to date the only means to study the crystal structure of tubulin. Also, our crystal structures are systematically considered in the light of thorough biochemical analysis. To bridge the gap with the in vivo polymerization, we are also gradually complexifying the system by the addition of critical components (Tau, kinesins) in a « divide and conquer » approach to cellular structural biochemistry. Group « Cytoskeleton dynamics and motility » The laboratory appreciates the excellent evaluation of this group and asserts its recognition of the quality of its research and international visibility of its PI. The director will conduct a reflection with the PI and the members of the group to envisage its evolution in the mid-term and maintain its scientific excellence.