Linum usitatissimum protoplast-derived colonies that are cultured in auxin-supplemented medium and immobilized in Ca(2+)-alginate matrix form round colonies that develop into polarized, embryo-like structures. On the other hand, protoplast-derived colonies that are immobilized in agarose do not show an organized morphogenetic response, and unique, ionically bound cell-wall protein patterns match this response. Although only slight differences in neosynthesized or total constitutive polypeptides are observed, dramatic changes in ionically bound cell-wall proteins are seen. In protoplasts grown on Ca(2+)-alginate-solidified, auxin-containing medium, several basic polypeptides were strongly induced and were found tightly bound to the cell wall. In contrast, these basic proteins were found only weakly bound to the walls of protoplasts grown on agarose-solidified, auxin-containing medium or on Ca(2+)-alginate-solidified, auxin-free medium, in which they were released into the medium. Our results suggest that plant cells can perceive and respond to the adjacent extracellular matrix, since we show that the growth of flax cells on Ca(2+)-alginate in the presence of auxin-containing medium may promote the binding of specific proteins to the walls. This establishes a direct correlation of an embryo-like morphogenesis with ionically bound cell-wall basic proteins in flax protoplasts grown on Ca(2+)-alginate-solidified, auxin-containing medium.