Annotation. The biodiversity of bacterial genomes is already reflected in the limited number of available genomes (almost 100 have been sequenced already and between 100 and 200 genomes are currently being sequenced). While at the level of protein sequence, enzymes for many central metabolic biosynthetic and biodegradative pathways are conserved, many deduced products of the so-called orphan genes, cannot be assigned a function at present, which probably reflects our inability to access the function from a biochemical point of view or to analyse the microorganism in the proper context, e.g. a number of orphan genes in Pseudomonas putida were assigned a role in attachment to plant roots, once this phenotype was analysed. Many genes have been annotated as belonging to complex families (i.e. membrane transporters, DNA binding proteins). Efforts to improve annotation and experimental set up (through high throughput techniques) need to be made to approach the question of the genomes from a global point of view. In this regard new algorithms are currently being developed and are expected to have great impact in the area of bioinformatics in the next few years. This workshop represents a unique oportunity to explore this issue in detail.
The global genome. Current annotation programmes are revealing our limited knowledge of the microbial world, but things should not come to a halt and the next obvious question should be 'how many genes actually exist'? We can hypothesize that, given the significant overlap between genes found in the many ongoing sequencing projects, the biosphere contains a large (yet finite) number of different genes. Such a gene pool would form a kind of global genome. As we continue to sequence organisms, the number of new genes discovered in each new genome becomes progressively fewer: the law of diminishing returns. On the other hand, it is likely that the greatest philogenetic, functional, and hence genetic diversity is represented in the currently unculturable members of the microbial world. We will always face the situation of unknown function (orphan genes) - a problem for which no easy solution is yet forseen. An approach for dealing with the challenge of discovering new genes (and thus sizing diversity) could be to focus future sequencing efforts not so much on microbial isolates but on the so-called meta-genomic DNA libraries. These libraries are prepared from pools of DNA that has been directly extracted from a given ecosystem (i.e. natural biofilm, waste waters, soil, rhizosphere, etc.) colonized by a given microbial community -without a need to worry about the original hosts of this DNA. Libraries of this sort recreate the gross genetic potential of a given ecosystem.
From the meta-genome to supra-metabolism? As a reflection on how intricate the management of diversity is, over the last 60 years microbiology journals have published thousands of reports on single-case examples of degradation of compounds by single bacterium or microbial communities. The problem is that the information from one case cannot simply be translated directly onto the next. Data on the biological catabolism of toxic pollutants is dispersed across a large variety of publications dealing with multifaceted genetics, biochemistry and ecology of a given compound in an entirely non-systematic form. Although we have reliable information on the microbial degradation of about 650 compounds, 450 catabolic enzymes and about 700 reactions of environmental interest, we are still unable to predict the fate and effects of many toxic compounds. In this context, it would therefore seem imperative that we develop ways of quantifying and formatting available information. Systems for automatic extraction of biodegradation-related (or otherwise) data from published scientific texts, abstracts and articles have to be developed. Such information should be shaped in a format that computers can manage so that massive comparisons of data can be undertaken and the possibility of system integration (for instance, the performance of a supra-metabolism) is explored.
When facing biosynthetic pathways, i.e. synthesis of fatty acids, amino acids, etc., gene diversity is also wide but not as much as with catabolic ones. In general, the prediction of these biosynthetic pathways is easier and in many cases can be delineated; however, many genes that should be in (and that are in) are not revealed by searching programmes, and some others that should not be included are. No doubt that this will open new research avenues in metabolomics.If we place the microbiology world in a specific niche, i.e. the plant rhizosphere or the animals' gut, not only single microbes are important, their interactions are too. A genomic approach can yield views on gene transfer, biofilm construction, cell-to-cell communication and saprophytic and detrimental interactions. These issues can now be approached from the genomic and meta-genomic world.
The hosting of this Workshop will contribute to overcome the notion of prokaryotes as simple models and will divulge their use in tackling more complex problems, and to reveal the microbial world as a genuine source of pivotal biological questions, involving many environmental and health problems, and which deserve a specific focus by themselves.
Venue:
Congress Palace, Granada, Spain
Dates:
November, 2004 (dates to be confirmed)
Programme:
Tentative speakers list:
S. Andersson (U. Uppsala).
Genome comparisons from an evolutionary perspectiveA. Bairoch (Swiss Prot., U. Geneva)
The HAMAP project at the Swiss ProtO. Beja (Haifa, Israel)
Rhodopsines in marine bacteriaP. Bork (EMBL, Heidelberg,)
The string programme and its implications for metabolism in bacteriaI. Cases (EBI, Cambridge)
Genomic descriptors of bacterial lifesylesV. de Lorenzo (CNB-CSIC, Madrid)
Grammar and promotersL. Duret (Lyon University)
Metabolomic of soil bacteriaS. Harayama (Biotechnology Center, Tokyo)
The complex genome of actynomycetes with biodegradative propertiesM. Holden (Sanger Center)
The world of StreptomycesD.R. Lovley (Amherst University)
The genome of a geobacteria that respires metalsJ.L. Ramos (EEZ-CSIC, Granada)
Bact-T-Regulators databaseC. Schleper (U. Darmstadt)
Accessing the genome of non-culturable bacteriaC. Thomas (University of Birmingham, U.K.)
Horizontal gene transferK.N. Timmis (GBF, Braunschweig)
Sequencing of halodegrading bacteriaB. Tummler (U. Hannover)
The genome of pathogenic and non-pathogenic strains of the same genusA. Valencia (CNB-CSIC, Madrid).
The organism-like behavior of the global biodegradation networkP. Williams (University of Nottinghan, UK)
Cell-to-cell communication
Registration:
For registration please go to workshop website