CONTENTS Page MAIN SYMPOSIUM Exploiting Genomes: Bases to Megabases in 50 Years 3 Offered papers (Poster) 6 GROUP SYMPOSIUM Cells & Cell Surfaces Group: Symposium: Microbial sensing and signalling 13 Offered papers (Poster) 14 Education & Training Group / Systematics & Evolution Group: Symposium: Making sense of bioinformatics: seeing the wood for the trees 19 Offered papers (Poster): Education & Training Group 21 Systematics & Evolution Group 21 Environmental Microbiology Group / Food & Beverages Group Joint Meeting Symposium: DNA-based detection methods 25 Offered papers (Poster): Environmental Microbiology Group 28 Food & Beverages Group 32 SGM Eukaryotic Microbiology Group / British Mycological Society / British Society for Medical Mycology Symposium: Post genomics applied to processes: advances in eukaryotic microbiology 37 Offered papers (Poster) 41 Fermentation & Bioprocessing Group Symposium: From molecular genetics, design and application to manufacturing 45 and regulatory issues of DNA at large scale Offered papers (Poster) 46 Microbial Infection Group: Symposium: Bacterial gene expression in vivo 47 Offered papers (Poster) 50 Physiology, Biochemistry & Molecular Genetics Group Symposium: DNA 1953-2003: from structure to function 61 Offered papers (Poster) 62 YOUNG MICROBIOLOGIST OF THE YEAR 71 INDEX OF AUTHORS 75 LATE ENTRIES 79 Society for General Microbiology – 153rd Meeting – UMIST, Manchester – 8-11 September 2003 - 1 - Society for General Microbiology – 153rd Meeting – UMIST, Manchester – 8-11 September 2003 - 2 - MAIN SYMPOSIUM Exploiting Genomes: Bases to Megabases in 50 Years Monday 8 September 2003 example abortions in cattle. Yet other species have evolved elaborate interactions with plants; in this group we find both 0905 Genomes and beyond plant symbionts and parasites. The recent sequencing of more GEORGE WEINSTOCK than 10 alpha-proteobacterial genomes, including our own Human Genome Sequencing Center, Baylor College of recently completed genomes form Bartonella , provides an Medicine, Houston, Texas, USA excellent opportunity for a global genomic comparison of human, With over 100 completed microbial genomes in the public animal and plant- associated bacteria. Here, we present the domain, the field of microbial genomics is in full bloom. phylogenetic relationships of the alpha-proteobacteria for which Although whole genome sequencing of microbes is still evolving, complete genome sequence data is available and discuss genomic it is now generally considered routine and uncontroversial, a features that are shared between human, animal and plant radically different view from less than a decade ago. But while pathogens. We identify differences in genomic contents and production of genome sequences is routine, the conversion of this architectures that correlate with major lifestyle changes. For sequence data into biologically meaningful information is at an example, we show that extreme genome size expansions of a few earlier stage of development. Bioinformatics tools for mining the thousand genes have occurred during the evolution of plant- genome and molecular genetic techniques for large-scale associated bacteria. In contrast, reductions of a few thousand analyses are being refined and more widely applied. These issues genes are characteristic of shifts to intracellular animal will be illustrated with the analysis of Treponema pallidum, the environments and vector-mediated transmission pathways. The spirochete that causes syphilis. This bacterium cannot be grown observation is that generation times, population sizes and outside of animal hosts, and thus many genetic and biochemical vulnerability to attack are major determinants for the genomic methods are difficult or impossible, making it both a natural evolution of bacteria that have developed close interactions with target as well as a challenge for genomic analysis. The genome plants and animals. sequence has been determined and analyzed bioinformatically, all the genes have been cloned and expressed in E. coli, attempts at 1330 Alternative splicing in mouse transcription vaccines and immunodiagnostics have shown promise, and whole factors – a genomic view genome comparisons with related spirochetes have been T. GAASTERLAND performed by several methods. These and other results will be Rockefeller University, New York, USA reviewed to present a picture of the present and future directions The application of gene identification methods to recently in microbial genomics research. completed genomes from multi-cellular organisms (C. elegans, Arabidopsis, Drosophila , M. musculus, H. sapiens) has revealed 0945 Comparative genomics of bacterial pathogens relatively small differences in the number of genes encoded by JULIAN PARKHILL these genomes. Subsequent EST- and cDNA-based studies The Sanger Institute, Wellcome Trust Genome Campus, indicate that an important factor in the complexity of the Hinxton, Cambridge, GB10 1SA - Email: eukaryotic proteome is multiplicity of gene structure: a single [email protected] gene gives rise to developmental stage-, tissue type- and As a group, the bacterial pathogens of humans are highly diverse, activation state-specific isoforms. Up to 59% (Lander et al 2001) both in terms of their phylogeny, and their strategies for taking of human and 33% (Brett et al 2002) of mouse genes have advantage of the opportunities offered by the human host. In alternative splice forms, and a recent analysis of a set of 60,000 contrast, many diverse diseases are caused by groups of related full-length mouse cDNAs indicates that the proportion may be as pathogens, and often strikingly different pathologies can be high as 68% (Zavolan et al 2002b). Another substantial finding caused by very closely related bacteria. Equally, the host ranges of the full-length cDNA sequencing projects is the frequent use available to related pathogens can vary widely. This spread of of alternative promoter and polyadenylation sites (Suzuki et al interactions between genotype and phenotype provides great 2001, Fantom consortium 2002) which is often associated with opportunities for using comparative genomics to investigate the alternative splicing of initial and terminal exons (Zavolan et al evolution and pathogenic strategies of these organisms. These 2002). concepts can be illustrated by comparisons amongst the Enteric Motivated by the Riken set full-length mouse cDNA became pathogens; Salmonella, Escherichia and Yersinia . These and available, we developed a systematic approach to characterize other examples will be discussed. splice variation as revealed by cDNA-to-genome mapping. A focus on full-length cDNA sequences reveals the full spectrum of 1100 Molecular profiling for diagnosis of infection variations generated in vivo, rather than having to combine data P. GHAZAL from multiple EST sequences. We developed computational University of Edinburgh Medical School methods to identify splice variants while eliminating variation High throughput technologies, such as microarray-based DNA, that was possibly due to cloning, sequencing and mapping errors. RNA and protein detection, have opened new fields in genomics To assess the potential effect on the proteome of alternative and proteomics. This talk aims to highlight the potential value splicing events cataloged in the previous section, we aligned the and limitation of this methodology, to design and extract 1667 cDNA sequences in the 581 variant clusters to the protein signature-based markers for infectious disease. sequences in the NR section of the Genbank sequence repository. we found that most of the splice variation occurs inside the 1145 Comparative genomics of alpha-proteobacteria coding region (68.1%). Only 11.6% and 20.4% alternative SIV G.E. ANDERSSON, CAROLIN FRANK, OLOF splicing events occur in the 5'- and 3'-UTR, respectively. As a KARLBERG, BASTIEN BOSSEAU, CHRIS COOPER, case study, we queried the database to retrieve Riken clones MAXIME HUVET & BORIS LEGAULT annotated with the keyword phrases “transcription factor” or Dept of Molecular Evolution, Evolutionary Biology Center, “DNA-binding”. 314 genomic clusters were retrieved, of which Uppsala University, Norbyvagen 18C, 752 36 Uppsala, 221 contained a variant exon, and 93 contained no variant exons. Sweden Next, we established whether the alternative splicing event was Members of the alpha-proteobacteria display a broad range of inside the coding sequence or in 5’ or 3’ untranslated regions. interactions with higher eukaryotes. Some are pathogens of Checking 10% (30 clusters), 70% of the variants influenced the humans that cause diseases such as typhus, trench fever and cat coding regions, and 25% of those affected the protein in frame scratch disease, while others are animal pathoges, causing for within a functional domain, as defined by SMART (Schultz et al Society for General Microbiology – 153rd Meeting – UMIST, Manchester – 8-11 September 2003 - 3 - 1998). The figure below illustrate exons mapped to the mouse approaches and data from expression studies. It has proved genome for one such transcription factor. essential to set gene annotation exercises in a strong virological context. Tuesday 9 September 2003 0900 Prediction of highly expressed genes in sequenced prokaryotic genomes DAVID W. USSERY , KOMPELLA ROHINI, CARSTEN FRIIS, PEDER WORNING & SØREN BRUNAK Microbial Genomics Group, Center for Biological Sequence Analysis, Building 208, Technical University of Denmark, DK-2800 Denmark The majority of genes in bacterial genomes