DNA macroarrays of 279 genes of Xanthomonas axonopodis pv. citri potentially associated with pathogenicity and virulence were used to compare the transcriptional alterations of this bacterium in response to two synthetic media. Data analysis indicated that 31 genes were up-regulated by synthetic medium XVM2, while only 7 genes were repressed. The results suggest that XVM2 could be used as an in vitro system to identify candidate genes involved in pathogenesis of X. axonopodis pv. citri. Within the genus Xanthomonas, several genes have been found associated with pathogenicity and virulence. Of these genes, the avr (avirulence), rpf (named for regulation of pathogenicity factors), and hrp (named for hypersensitive response and pathogenicity) genes are perhaps the most widely studied elements. The avr genes encode a known group of effector proteins responsible for controlling the ability of bacteria to elicit the hypersensitive reaction in resistant hosts (26) and may also participate in pathogenicity or virulence in compatible interactions (38,47). The rpf operon is thought to control the production of important pathogenicity factors, such as proteases, endoglucanases, polygalacturonate ligases, and extracellular polysaccharides (5, 17). Finally, the hrp genes are thought to encode proteins involved in the type III secretion system, responsible for delivering effector proteins inside the host plant cells (8,9,20,21).Even though pathogenicity and virulence of Xanthomonas axonopodis pv. citri have been traditionally associated with the activity of a single avirulence-like gene known as pthA (14,22,45,46), little is known about other gene products involved in these processes. In this respect, transcription profiling under natural conditions may be a good alternative to identify all the elements involved in pathogenicity and virulence of this microbial pathogen. However, leaf spot pathogens, such as X. axonopodis pv. citri, do not reach high population levels in infected tissues and do not yield enough material (either bacterial cells or RNA) to conduct gene expression studies. Therefore, in an attempt to develop an alternative system for gene expression studies, an in vitro system was evaluated in order to determine whether it could be used to model pathogen responses to host tissues under controlled conditions. The two media selected were NB (nutrient broth), commonly used for growing this bacterium, and XVM2, suspected to mimic the environment of the plant intercellular spaces (1, 41, 51, 55).Construction of DNA macroarrays. To study the expression profile of X. axonopodis pv. citri, 279 candidate genes, associated with pathogenicity or virulence by sequence similarity, were selected from the genome of this bacterium (13). Specific primers were designed to amplify either the entire open reading frame or a fragment of it. PCR amplifications were performed in two rounds using 96-well plates and a Mastercycler Eppendorf (Eppendorf). The quality of amplimers was analyzed by agarose gel electrophoresis.Prior to the cons...