Bacterial panicle blight caused by Burkholderia glumae is a major bacterial disease of rice. Our preliminary RNA-seq study showed that a serine metalloprotease gene， prtA， is regulated in a similar manner to the genes for the biosynthesis and transport of toxoflavin， which is a known major virulence factor of B. glumae. prtA null mutants of the virulent strain B. glumae 336gr-1 did not show a detectable extracellular protease activity， indicating that prtA is the solely responsible gene for the extracellular protease activity detected from this bacterium. In addition， inoculation of rice panicles with the prtA mutants resulted in a significant reduction of disease severity compared with the wild type parent strain， suggesting the requirement of prtA for the full virulence of B. glumae. A double mutant deficient in both serine metalloprotease and toxoflavin (ΔtoxA/prtA-) exhibited a further numeric but not statistically significant decrease of disease development compared with the ΔtoxA strain. Both the prtA-driven extracellular protease activity and the toxoflavin production were dependent on both the tofI/tofR quorum-sensing (QS) and the global regulatory gene qsmR， indicating the important roles of the two global regulatory factors for the bacterial pathogenesis by this pathogen.