Report from the visiting committee

Transcription

1 Section des Unités de recherche Report from the visiting committee Research unit : Génétique et Microbiologie UMR_A 1128 University Henri Poincaré - Nancy 1 February 2008

2 Section des Unités de recherche Report from the visiting committee Research unit : Génétique et Microbiologie UMR_A 1128 University Henri Poincaré Nancy 1 February 2008

3 Report from the visiting committee The research unit : Name of the research unit : Génétique et Microbiologie Requested label : UMR_A N in case of renewal : 1128 Head of the research unit : Mr Pierre LEBLOND University or school : University Henri Poincaré -Nancy 1 Other institutions and research organization: INRA Date(s) of the visit : February 8,

4 Members of the visiting committee Chairman of the commitee : Mr Ivan Matic Other committee members : Mr Meriem El Karoui Mr Keith Chater Mr Ingolf Nes Mr Wolfgang Wohlleben CNU, CoNRS, CSS INSERM, représentant INRA, INRIA, IRD..) representatives : Mrs Marie-Claire Lett, CNU representative Observers AERES scientific representative: Mrs Alexandra Gruss University or school representative: Mr Pierre Mutzenhardt, Université Nancy 1 Research organization representative (s) : Mr Claude Gaillardin, INRA 3

5 Report from the visiting committee 1 Short presentation of the research unit Number of lab members : 23 including : - researchers with teaching duties (8), - full time researcher (1), - Post-doc (1), - PhD Students (5), - master students (4), - technicians (3.66) and administrative assistant (0.5)] Number of HDR and of HDR who are PhD students advisors : 4 among which 3 supervise students Number of PhD. Students who have obtained their PhD and average length of a PhD during the past 4 years: 11 between 2003 and present (average length 4 years) Number of PhD students currently present in the research unit : 5 Number of PhD students with fellowships: 3 MRT, 2 collectivité territorial Number of lab members who have been granted a PEDR : 4 Number of «publishing» lab members : 9/9 EC, C 2 Preparation and execution of the visit The evaluation was very well organized, which allowed the committee members to work under excellent conditions. After an introductory presentation by the laboratory director, senior researchers and PhD students from the two teams presented their scientific activity. The choice of the speakers, as well as the quality of presentations and of discussions, provided very good insight into the most important results and the research projects to the evaluation committee. The discussion with laboratory staff belonging to all professional categories about laboratory organization and human relationships was useful, as it permitted to have a complete insight into how this research unit functions. 3 Overall appreciation of the activity of the research unit, of its links with local, national and international partners This laboratory is composed of two research teams entitled: Genome plasticity & mechanisms of adaptation and Chromosome dynamic & biosynthesis of secondary metabolites. The first team uses Streptococcus thermophilus and Streptococcus agalactiae as model organisms, while the second team studies Streptomyces ambofaciens. Both types of organisms have the benefit of having applied interest: Streptococci are important in the food industry, and as pathogens; and streptomycetes are the major industrial producers of antibiotics and related substances. A recently constructed L2 confinement laboratory allows work with the pathogenic bacteria. 4

6 The common research interest of the two teams is bacterial genome structure, horizontal gene transfer (HGT) and the impact of HGT on the adaptation of recipient organisms to biotic and abiotic environments. For the future, three research themes were abandoned according to the recommendation of the previous evaluation committee in order to avoid thematic dispersion. By using multidisciplinary approaches: comparative genomics, functional analysis of HGT mechanisms and of transferred genes, data mining and bio-informatics, the members of this laboratory have successfully achieved their main scientific goals during last four years. Both groups have generated original and exciting results that have been published, although only in specialized journals. This definitely does not reflect the scientific quality of their research. Given the originality of their as yet unpublished results and quality of the research projects, it is very likely that they can publish in higher impact journals. Quantitative aspects of the scientific production (21 research article & 2 review articles in last four years) must be analyzed in light of the fact that eight out of nine permanent staff members have heavy teaching duties, which significantly reduces the time they can allocate to research activities. Besides other teaching duties, the members of this laboratory are actually creating a new Masters program with two specialties: Microbial biotechnologies and Environmental and sanitary microbiology. The laboratory has recently left BioSE doctoral school for RPPE doctoral school, which is more focused on microbial ecology and applied research. The links between the laboratory and its immediate environment, i.e., University and IFR, are beneficial for the laboratory. Most of the permanent staff are University employees, while IFR provides access to many technical platforms (DNA sequencing and high-throughput genomic analyses facilities, confocal microscope etc.). The laboratory also collaborates with other research units belonging to the same IFR. This research unit is UMR University/INRA. The research activities of this laboratory are attached to the INRA strategic axes CT1 and CT2. INRA provides small funding and the salary of one permanent researcher. Bioinformatics projects concerning analysis of streptomycetes and streptococci genomes are developed mainly in collaboration with LORIA (INRIA, Nancy) and to a lesser extent with MIG (INRA, Jouy en Josas). The work of this laboratory is nationally and internationally recognized as suggested by the invitations of its members to speak at national and international meetings, as well as by the group s involvement in major international projects. The laboratory has also obtained regional and national grants. 4 Specific appreciation team by team and/or project by project Research team 1: Genome plasticity & mechanisms of adaptation Studies includes : - Horizontal gene transfer in streptococci with emphasis on Integrative and Conjugative Elements (ICEs); - Adaptation of S. thermophilus to the environment, in particular the role of Rgg transcriptional regulators. Horizontal gene transfer in streptococci : The main objective of these studies is the determination of the mechanisms of evolution of the so-called genomic islands. The group has been focusing on DNA elements that can conjugate and integrate into the chromosome and proposed a typology for these elements introducing the generic term of ICEs. It has been shown that such elements have evolved by acquisition or exchanges of modules (involved in regulation, conjugation or integration). A convincing model of the evolution of ICEs and CIMEs (cis Mobilisable Element) by site-specific accretion, deletion and cis-mobilisation has been proposed. The group mostly focuses on the analysis of the S. thermophilus ICEs, mainly ICESt1 and ICESt3. Site-specific excision, integration and conjugative transposition of these ICEs have been proven to take place. The modules encoding putative regulatory proteins of ICEs (in particular arp1) have been identified. Future work involves detection of cis acting mobilization and in depth analysis of regulation of ICE s recombination/conjugation modules. By using bioinformatics tools, i.e., Hidden Markov Models, this group has detected regions with atypical nucleotide composition (an indication of HGT). Analysis of the S. thermophilus genome allowed the detection of 49 regions, among which some are likely to contain exogenous DNA (e.g. one cluster seems 5

7 to come from L. lactis). The group plans to develop an automated comparative analysis of the identified regions among firmicutes. The data will also be compared with variable regions detected with Comparative Genome Hybridization arrays in collaboration with an industrial partner. Recently, the analysis was extended to S. agalactiae. From the different S. agalactiae genomes investigated, 31 ICE-like elements were identified, which suggests that ICEs may contribute to the genomic plasticity as well as spreading of virulence genes in this species. This result provides a good opportunity to check whether atypical regions detected by the bioinformatics approach correlate with ICE elements already identified in this species through Blast analysis and manual curation. Future work involves testing the mobility of some of these elements and characterization of new ICEs in strains isolated from animal infections. Adaptation of S. thermophilus to the environment : This research group has identified a number of genes involved in response to oxidative stress, among which the gene cse encodes an extracellular protein that was shown to be involved in cellular segregation and cell morphology of S. thermophilus. Of particular interest is the involvement of 7 putative regulatory genes called rgg whose distribution is variable among strains and that show a high level of polymorphism. Deletion analysis suggests that at least some of them are involved in oxidative response. Future work involves characterisation of the phenotype of mutants and identification of the mechanisms of rgg activation, possibly though quorum sensing. Strengths : This is a relatively small group (5 permanent researchers, 4 having heavy teaching duties) but with its good dynamics and direction, it appears to work well. Their work has significantly contributed to new ideas of how horizontal gene transfer takes place and contributes to the genomic diversity. In particular, this group is in a unique position to investigate the role of ICEs elements in the genomic diversity of streptococci and the potential consequences on development of pathogenicity of some species. The group has publications in the best specialized microbial journals (Mol Mic, JBacteriol, Microbiol, AEM). Weaknesses : Despite conceptual new findings and many exciting results obtained (identification of ICEs, etc..) the group has not gained an international strong position. In our view this does not reflect the quality of the results. In silico detection of horizontal gene transfer is a very competitive field. Therefore, the originality of the approach developed here will certainly depend upon careful biological interpretations of the data, as well as upon the uniqueness of the biological systems under study. Recommendations : The committee supports the development and strengthening of the work on ICEs in streptococci with emphasis on their consequences for genomic stability and gene transfer both within species as well as between species/genera. Extension to pathogenic streptococci is also supported. The study of the rgg regulatory system would benefit from careful examination and re-centering of the subject on the very interesting phylogenetic distribution of this still poorly understood regulatory system. For example, they should exploit the existence of 7 rgg genes in Streptococci. However if not more resources (post docs and PhD students) are allocated to the group it may be wiser for the team to join efforts and to keep to a more narrow focus on some of the aspects of the ICEs. It is recommended that a concerted effort be made to improve the level (for the Rgg work) and/or numbers (for both subjects) of publications. Research team Chromosome dynamic & biosynthesis of secondary metabolites began to study genetic instability long before genome sequencing became available. Now, this study has naturally become highly dependent on genome-scale sequence information, and is genome-led rather than phenotype-led as in its earlier stages. A major effort has been the sequencing of the arms of the S. ambofaciens chromosome, and work continues to complete the entire genome sequence. This will be of considerable value in relation to the existing complete sequence of the more widely used model organism S. coelicolor, since the two species are very closely related: The comparison will therefore further illuminate our understanding of genome flux over relatively short evolutionary time. In the meantime, the analysis of the chromosome arms has revealed that the variable ends (variable mainly in relation to other Streptomyces genomes, but also significantly variable within the span of laboratory experiments) and 6

8 conserved core are separated by an extended boundary region with a gradient of variability. This group has also used bioinformatics approaches to predict regulatory motifs recognized by sigma factors, which are very numerous in streptomycetes. Two approaches have been developed : one based on the use of Hidden Markov Models and the other on statistical detection of over-represented motifs. Future work, involving clever technology to generate double-strand breaks at predetermined locations, will explore whether this involves regional physiological/biochemical differences in recombination and double-strand break repair mechanisms. This will presumably require the laboratory to acquire the appropriate biochemical expertise. The interesting questions of whether the chromosome ends are preferentially transferred, and whether there are environmental (ecological) triggers for transfer, will also be addressed. As far as we know, these questions are not being addressed anywhere else in the world, but they may well have an impact on the way that other workers think about their results on other streptomycetes. One could argue that this work might be more mainstream if done with S. coelicolor, but there is also a compelling argument that the discoveries in S. ambofaciens will have greater resonance because of their comparison with S. coelicolor, and thus their generalisability to most streptomycetes will be quickly perceived, which would not happen if the work were done first in S. coelicolor. An important emerging theme is secondary metabolism, a theme shared by many other laboratories. Investigation of secondary metabolite biosynthesis pathways focuses on two clusters of S. ambofaciens: alp and unidentified PKSI-product. Both clusters have interesting features and analysis of the clusters may lead to results of general interest and should therefore be carried out. For biochemical and chemical aspects of the biosynthesis as well as for combinatorial approaches it is important that the laboratory establishes cooperations. It is difficult to know at this stage whether the clusters being studied will prove valuable in a therapeutic context. Strengths : The committee was impressed by the coherence of the group (3 permanent researchers + one post-doc) and its programme. The group holds a special position internationally, because it is the only Streptomyces group whose primary concern is genome analysis most other laboratories focus on more physiological aspects of the organisms, and acquire and use genome information mainly in the service of those interests. This focus on genomics is valuable (the resource of genome sequences for comparative genomics would otherwise be significantly wasted). The group s involvement in a major EU project is quite important this ensures that there is good cross-talk with workers on other members of the Streptomyces genus, maximising the influence of the work (without this kind of contact, there would be a danger that S. ambofaciens could be marginalised, since it is not much studied outside of France). The work is evidently held in high regard, since it was represented by invited papers at the two major international symposia for actinomycete biologists (GIM, Prague, 2006; ISBA, Newcastle, 2007). The forward programme looks well-planned - there is likely to be a substantial need for and interest in genome analysis for the foreseeable future, which will put the lab in a strong position without the need to diversify into more physiologically-based studies (i.e., beyond the work already initiated on secondary metabolism). Weaknesses : Although the focus on genomics is valuable it probably makes access to the most highly ranked journals relatively difficult: A view that is reflected in the fact that the group s papers are mostly in the leading specialist microbiology journals. The labs skill range is largely limited to molecular genetics, making it potentially difficult to extend into physiological and biochemical areas. Recommendations : The strength in comparative genomics and genome-based analysis should be exploited to increase the outwardlooking face of the laboratory. Substantial long-term interaction with a more-or-less dedicated bioinformatician at Nancy would be necessary to achieve this aim. It will be important to ensure that suitable long-term collaborations are in place to permit the laboratory to remain competitive when the experimental demands fall outside of skills possessed by the lab. This is likely to apply in both studies of recombination and repair, and of biosynthesis of secondary metabolites. Further diversification into more physiologically-based studies should be undertaken only in response to very strong opportunities and interest. 7

9 5 Appreciation of resources and of the life of the research unit The new director of the laboratory (since June 2007) has maintained very positive working atmosphere. In spite of heavy teaching duties, the members of the laboratory maintain regular weekly scientific meetings joining two groups. Staff belonging to all professional categories expresses very positive opinion about professional and human interactions in the laboratory. The technicians seem to be well integrated, and take turns for common duties. The group has an unbalanced composition of staff. Of nine permanent staff members only one is fully dedicated to research while the other 8 have a significant teaching load. PhD students have also teaching duties (64h/year). Actually, there is one post doc and 5 PhD students (formerly 10) in the laboratory. The decrease in the number of students is a problem that should be seriously considered. 6 Recommendations and advice Strengths : This laboratory consists of competent and dedicated staff members. In spite of heavy teaching duties of most of the permanent researchers and even PhD students, the laboratory is dynamic and productive. The technical staff seems to be well integrated in the scientific life of the laboratory. The direction seems to constantly evaluate feasibility and priority of different projects as a function of available work manpower in order to avoid dispersion and to increase efficiency and quality. Consequently, some projects are abandoned, which is usually a difficult decision to be taken. Harmony between the two research themes is assured by interactivity and common laboratory meetings. Their work has significantly contributed to new ideas of how horizontal gene transfer takes place and contributes to the genomic diversity in streptococci. In particular, this group is in a unique position to investigate the role of ICEs elements in the genomics diversity of streptococci and the potential consequences on development of pathogenicity. The Streptomyces group holds a special position internationally, because it is the only group whose primary concern is genome analysis. The forward programme looks well-planned. The bioinformatic projects are very well connected with the biological questions addressed in the laboratory. They will therefore benefit from the knowledge developed in the experimental projects. Research projects in the areas of microbial biodiversity are coherent with the organisms forming this mixed unit. The laboratory publishes in the best specialized microbial journals. Weaknesses : Primary weakness is in the fact that the most of the permanent researchers and even the PhD students have heavy teaching duties. The decrease in the number of PhD students and small number of post-docs is a problem that should be seriously considered. Despite conceptual new findings and many exciting results obtained, the group has not gained merited international strong position. The laboratory skill range is largely limited to molecular genetics, making it potentially difficult to extend into physiological and biochemical areas. 8

10 Recommendations : The strength in comparative genomics and genome-based analysis should be exploited to increase the outwardlooking face of the laboratory. Substantial long-term interaction with a more-or-less dedicated bioinformatician at Nancy would be necessary to achieve this aim. It will be important to ensure that suitable long-term collaborations are in place to permit the laboratory to remain competitive when the experimental demands fall outside of skills possessed by the lab. If not more resources (post docs and PhD students) are allocated to the group it may be wise to concentrate efforts on the most exciting projects. A more aggressive strategy for promoting the science performed by the group such as publication in higher impact journals and more active promotion of research at relevant scientific conferences may improve the group s international recognition. 9

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