What can bacterial genome research teach us about bacteria–plant interactions? Alfred Pu ¨ hler 1,5 , Matthieu Arlat 2 , Anke Becker 1 , Michael Go ¨ ttfert 3 , John P Morrissey 4 and Fergal O’Gara 4 Biological research is changing dramatically. Genomic and post-genomic research is responsible for the accumulation of enormous datasets, which allow the formation of holistic views of the organisms under investigation. In the field of microbiology, bacteria represent ideal candidates for this new development. It is relatively easy to sequence the genomes of bacteria, to analyse their transcriptomes and to collect information at the proteomic level. Genome research on symbiotic, pathogenic and associative bacteria is providing important information on bacteria–plant interactions, especially on type-III secretion systems (TTSS) and their role in the interaction of bacteria with plants. Addresses 1 Lehrstuhl fu ¨ r Genetik, Universita ¨ t Bielefeld, 33594 Bielefeld, Germany 2 Laboratoire des Interactions Plantes Microorganismes, INRA/CNRS, BP 27, 31326 Castanet Cedex, France 3 Institut fu ¨ r Genetik, TU Dresden, Mommsenstrasse 13, 01062 Dresden, Germany 4 BIOMERIT, Department of Microbiology, University College Cork, Ireland 5 e-mail: puehler@genetik.uni-bielefeld.de Current Opinion in Plant Biology 2004, 7:137–147 This review comes from a themed issue on Genome studies and molecular genetics Edited by Joseph R Ecker and Doug Cook 1369-5266/$ – see front matter ß 2004 Elsevier Ltd. All rights reserved. DOI 10.1016/j.pbi.2004.01.009 Abbreviations avr avirulence gene GI genomic island ORF open reading frame PGPR plant-growth-promoting rhizobacteria Pst Pseudomonas syringae pv. tomato Rs Ralstonia solanacearum TTSS type-III secretion system Xac Xanthomonas axonopodis pv. citri Xcc Xanthomonas campestris pv. campestris Xf Xylella fastidiosa Xf-ALS X. fastidiosa strain Dixon Xf-CVC X. fastidiosa 9a5c Xf-OLS X. fastidiosa strain Ann1 Xf-PD X. fastidiosa strain Temecula Introduction Bacteria–plant interactions can be subdivided into three classes: symbiotic, pathogenic and associative. The sym- biotic interaction is characterized by the formation of root nodules that are colonised by a microsymbiont. As a result, the microsymbiont is able to fix atmospheric nitrogen and to deliver fixed nitrogen to the macrosym- biont. Phytopathogenic interactions are more diverse. Phytopathogenic bacterial species have developed spe- cific methods to attack plant cells and to use plant sub- stances for their own growth. In the associative interaction, both the bacteria and the plant profit from each other. The bacteria live on plant exudates and either protect the plant by suppressing plant pathogens or stimulate plant growth by providing specific bacterial substances. Because bacteria–plant interactions play an important role in agriculture, a lot of effort has been put into analysing these interactions in detail. The first sequenced genome of a symbiotic bacterium was that of Mesorhizo- bium loti [1], followed by that of Sinorhizobium meliloti [2]. Amongst phytopathogenic bacteria, the genome of Xylella fastidiosa (Xf) [3] was the first to be sequenced. Sequenc- ing projects are underway for associative bacteria but none has been completed. Although the genomic sequences of plant-colonising bacteria have only been established recently, review articles that summarise and compare the findings already exist. The review by Van Sluys et al. [4] is an interesting article that compares the genome sequences of seven plant-colonising bacteria. The genomes included are those of Agrobacterium tumefaciens [5,6], M. loti [1], S. meliloti [2], Xanthomonas campestris pv. campestris (Xcc) [7], Xanthomonas axonopodis pv. citri (Xac) [7], Xf [3] and Ralstonia solanacearum (Rs) [8]. The article concentrates on genome structure and metabolic pathways. It high- lights type-III secretion systems (TTSS) for the control of host compatibility and reports on cell-wall-degrading enzymes and genes that are involved in overcoming the oxidative burst that is induced in the plant host. Another recent review, by Weidner et al. [9], deals with genomic insights into symbiotic nitrogen fixation. This article covers genomic aspects of both the micro- and the macrosymbiont, and concentrates on the interactions between M. loti and Lotus species and between S. meliloti and Medicago. Of special interest, this review article also reports on the use of transcriptomics and proteomics techniques to analyse the interaction between Rhizobium sp. NGR234 and S. meliloti. www.sciencedirect.com Current Opinion in Plant Biology 2004, 7:137–147