Plant cell wall degradation is a premier event when Bacillus subtilis, a typical saprophytic bacterium, invades plants. Here we show the degradation system of rhamnogalacturonan type I (RG-I), a component of pectin from the plant cell wall, in B. subtilis strain 168. Strain 168 cells showed a significant growth on plant cell wall polysaccharides such as pectin, polygalacturonan, and RG-I as a carbon source. DNA microarray analysis indicated that three gene clusters (yesOPQRSTUVWXYZ, ytePQRST, and ybcMOPST-ybdABDE) are inducibly expressed in strain 168 cells grown on RG-I. Cells of an industrially important bacterium, B. subtilis strain natto, fermenting soybeans also express the gene cluster including the yes series during the assimilation of soybean used as a carbon source. Among proteins encoded in the yes cluster, YesW and YesX were found to be novel types of RG lyases releasing disaccharide from RG-I. Genetic and enzymatic properties of YesW and YesX suggest that strain 168 cells secrete YesW, which catalyzes the initial cleavage of the RG-I main chain, and the resultant oligosaccharides are converted to disaccharides through the extracellular exotype YesX reaction. The disaccharide is finally degraded into its constituent monosaccharides through the reaction of intracellular unsaturated galacturonyl hydrolases YesR and YteR. This enzymatic route for RG-I degradation in strain 168 differs significantly from that in plant-pathogenic fungus Aspergillus aculeatus. This is, to our knowledge, the first report on the bacterial system for complete RG-I main chain degradation.Bacillus subtilis, the best-characterized gram-positive bacterium, is widely distributed and has various high levels of potential to incorporate external DNA; produce amino acids, antibacterial agents, and industrially important enzymes; secrete large amounts of proteins; form endospores; and associate with plants. The complete genome sequence for the type strain, B. subtilis 168, was determined in 1997, and about 4,000 genes were found contained in the bacterial genome (26). The clarification of function-unknown genes is now being focused on, and essential genes in the bacterium have been identified through the construction of knockout mutants for each gene (25). Although mechanisms for DNA uptake (10), amino acid fermentation (20), antibiotic production (49), protein secretion (49), and endospore formation (44) are well analyzed, little is known about the interaction between bacilli and plants.B. subtilis is important for producing fermented foods and for composting plants (41). In Japan, this bacterium is called "Kosoukin," which means "bacteria present in dead grass," and a type of B. subtilis, strain natto, has been used for the production of "natto" for over 1,000 years. Natto is produced through the fermentation of boiled soybeans by strain natto. Natto-like fermented soybean foods such as tempe and Thua nao are also produced in Asia and Africa. In natto production, cells of strain natto sprayed on boiled soybeans degrade their cell wall...