Proline (Pro) metabolism is important for environmental stress responses, redox balance, and plant growth. However, the mechanism of Pro in abiotic stress processes still remain to be elucidated. Using the atrzf1 mutant as a parental line for T-DNA tagging mutagenesis, we identified a suppressor mutant of atrzf1, designated proline content alterative 13 (pca13). The pca13 suppressed insensitivity of atrzf1 to water deficit stress during early seedling growth. In addition, Pro content in pca13 was lower than in that of atrzf1 under drought stress condition. By the TAIL-PCR, it was found that T-DNA of pca13 was inserted into the promoter of Rhamnogalacturonan Lyase 1 (RGLyase1), and the complementary lines showed sensitive phenotype similar to pca13 mutant under osmotic stress condition. Expression level of RGLyase1 was strongly induced by abscisic acid, osmotic, salt and oxidative stresses. Overexpression of RGLyase1 increased tolerance to osmotic stress, whereas rglyase1 RNAi displayed sensitive phenotype to osmotic stress. Furthermore, enzymatic assay indicated that RGLyase1 has rhamnogalacturonan lyase activity, which might suppress AtRZF1 by regulating xylem structure. Taken together, these findings prove that pca13 acts as a suppressor of atrzf1 in the abiotic stress responses through Pro and cell wall metabolisms.