Unit: Genetics of Bacterial Genomes
Director: Antoine DANCHIN
In collaboration with the Genoscope (CNRS) in Evry, the University of Liège and Naples, the Genetics of Bacterial Genomes Unit has completed the sequencing and annotation of the genome of a bacterium from Antarctica, Pseudoalteromonas haloplanktis TAC125. In parallel it further developed its studies of sulfur metabolism in Bacillus subtilis, solving several problems of transport of sulfur containing molecules, and of the methionine salvage pathway. Work in silico (with computers) allowed us to characterize further many components of the constraints that operate on the gene distribution in chromosomes. Moreover we uncovered ubiquitous rules in the distribution of amino acids in proteins. Our work aims at seing post-sequencing biology as symplectic (sun: together, plektein, to weave) biology, where the links between objects make the core of the discoveries to come.
Rather than considering the hereditary material as a simple collection of genes, the aims of genomics are to provide an understanding of the functional organisation of genes within chromosomes and to explain how this organisation produces life. Bacteria are ideal subjects for such studies because they have existed for a very long time (more than three thousand billion years of evolution) and are highly diverse. Understanding how genes interact makes it possible to evaluate more accurately the adaptive potential of bacteria, both in the environment and in and on our bodies (they are everywhere and our bodies contain at least ten times more bacteria than human cells). Despite the negative connotations associated with bacteria, the fashion for nutraceutics ("medical" foods) is based on the implicit idea that bacteria are more often beneficial, even if, on occasion, they are highly pathogenic. Surprisingly, there are few differences between commensal bacteria and the bacteria responsible for diseases. One of the aims of comparative genomics is to understand how differences in genome organisation can determine whether a bacterium is innocuous (or beneficial to the host) or virulent.
This requires, of course, reference models in which we understand practically all we can do about the organism. Two major classes of bacteria can be distinguished by a specific staining method developed by the Dane Christian Gram. Gram-positive bacteria are common in foods (lactobacilli and streptococci are present in yoghurts and cold meats, for example). In some cases, they may be pathogenic (Staphylococcus aureus). The model for these bacteria is Bacillus subtilis, for which the Unit has been a driving force behind genomic studies. Our current research aims to determine how the genes of this organism are organised, both by computer-based (in silico) studies based on the analysis of gene sequences and their products (mRNA and protein), and by the study of sulphur metabolism, which is highly structuring. We began by establishing a number of rules forcing genes to prefer one strand of DNA rather than the other. These rules are due to the exertion of a selection pressure that favours the progression of the transcription fork in the same direction as transcription, preventing conflicts leading to the production of truncated mRNA molecules, which in turn generate truncated proteins. Sulphur metabolism genes are grouped in functional islands. Within these islands, we recently characterised mostly genes encoding transport proteins and some of the proteins regulating their expression. We have now begun to extend our studies to pathogenic organisms of the same class. We have also characterised a little-known pathway - the methionine recycling pathway (all the proteins of living organisms begin with this amino acid) - which we have shown sometimes leads to the synthesis of an unexpected gas, carbon monoxide, which may act an intercellular signal, by means of currently unknown mechanisms.
Escherichia coli is the model gram-negative bacterium and is today the best understood organism in the world. As part of a transverse research programme, we analysed families of gram-negative bacteria in an attempt to determine what makes some bacteria beneficial and others not (for example, most strains of E. coli are harmless, but certain strains of E. coli cause colibacillosis, a well-known disease). We studied the determinants of pathogenesis in a related bacterium, Photorhabdus luminescens. This bacterium is extremely pathogenic in insects and would be highly dangerous to humans if it were able to grow at our body temperature, which is fortunately not the case. We characterised a series of genetic control systems, to identify the keys to the remarkable pathogenicity of this organism. This work will be continued in the next few years, using the silk worm as the host organism. One of the main advantages of this approach is that it enables us to study bacterial virulence without using mammals, whilst generating results that can be extrapolated to these animals.
The Unit has recently finished, in collaboration with Génoscope and the universities of Liège and Naples, sequencing and studying the genome of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC 125, which belongs to the same family of gamma-proteobacteria, as a means of exploring the physical constraints exerted on the construction of genomes. The genome sequence is currently being analysed, to investigate the effects of extreme cold on the distribution and composition of genes (this bacterium is the fastest growing known bacterium at low temperature). We are also exploring the possible biotechnological uses of growth at very low temperature.
At this stage of our genomic studies, it is essential to determine the distribution of the gene products in the cell. Studies on uridylate kinase carried out by the group of Anne Marie Gilles have provided interesting information in this area and an article on the three-dimensional structure of the protein has been submitted.
A major part of the work of the Unit involves organising the genomic data obtained for bacteria. In Hong Kong, where we are heading a programme financed by the Hong Kong government, we are involved in the construction of the Genochore family of databases for reference bacteria (http://bioinfo.hku.hk/genochore.html): 17 genome sequences are currently available from these databases, including that of a small eukaryotic organism, the parasite Encephalitozoon cuniculi.
Finally, in 2004, we analysed the epidemic of atypical pneumonia (SARS; severe acute respiratory syndrome) and were involved, with the epidemiological consortium of GuangDong (co-ordinated by Prof. Guoping Zhao from the Shanghai Genomic Centre), in a molecular study of the characteristics of the epidemic. The results obtained, which were very instructive and entirely compatible with the hypothesis of a double epidemic that we formulated in 2003, will be published in 2005.
Culture of Pseudoalteromonas haloplanktis TAC125, as viewed with an electron microscope.
Keywords: genomics, sulphur metabolism, nucleotide kinases, in silico, databases