A method for production of a heterologous soluble polypeptide by a ciliate, the method comprising: (a) transforming said ciliate with a nucleic acid encoding a fusion protein comprising from N-terminus to C-terminus: (i) a mucocyst-targeting polypeptide of a mucocyst-targeted protein which is cleaved by a protease endogenous to said mucocyst; and (ii) a heterologous polypeptide; wherein expression of said fusion protein results in trafficking of said fusion protein to mucocysts within said ciliate and cleavage of said mucocyst-targeting polypeptide to release said heterologous soluble polypeptide within said mucocysts; (b) stimulating regulated secretion from said mucocysts of said ciliate, whereby an extracellular matrix is formed; and (c) separating said heterologous soluble polypeptide from said extracellular matrix and said ciliates, or (a) transforming said ciliate with a nucleic acid encoding a first fusion protein comprising from N-terminus to C-terminus: (i) a heterologous polypeptide; and (ii) at least a mucocyst-targeting polypeptide of a mucocyst-targeted protein; wherein expression of said first fusion protein results in trafficking of said first fusion protein to mucocysts within said ciliate; and wherein an endogenous protease within said mucocysts cleaves a cleavage site within said mucocyst-targeting polypeptide and removes any sequences C-terminal to said cleavage site, thereby producing a second fusion protein within said mucocysts; (b) stimulating regulated secretion from said mucocysts of said ciliate, whereby an extracellular matrix is formed; and (c) separating said heterologous polypeptide from said extracellular matrix and said ciliates. (a) transforming said ciliate with a nucleic acid encoding a fusion protein comprising from N-terminus to C-terminus: (i) a mucocyst-targeting polypeptide of a mucocyst-targeted protein which is cleaved by a protease endogenous to said mucocyst; and (ii) a heterologous polypeptide; wherein expression of said fusion protein results in trafficking of said fusion protein to mucocysts within said ciliate and cleavage of said mucocyst-targeting polypeptide to release said heterologous soluble polypeptide within said mucocysts; (b) stimulating regulated secretion from said mucocysts of said ciliate, whereby an extracellular matrix is formed; and (c) separating said heterologous soluble polypeptide from said extracellular matrix and said ciliates, or (a) transforming said ciliate with a nucleic acid encoding a fusion protein comprising from N-terminus to C-terminus: (i) a mucocyst-targeting polypeptide of a mucocyst-targeted protein which is cleaved by a protease endogenous to said mucocyst; and (ii) a heterologous polypeptide; wherein expression of said fusion protein results in trafficking of said fusion protein to mucocysts within said ciliate and cleavage of said mucocyst-targeting polypeptide to release said heterologous soluble polypeptide within said mucocysts; (i) a mucocyst-targeting polypeptide of a mucocyst-targeted protein which is cleaved by a protease endogenous to said mucocyst; and (ii) a heterologous polypeptide; (b) stimulating regulated secretion from said mucocysts of said ciliate, whereby an extracellular matrix is formed; and (c) separating said heterologous soluble polypeptide from said extracellular matrix and said ciliates, or (a) transforming said ciliate with a nucleic acid encoding a first fusion protein comprising from N-terminus to C-terminus: (i) a heterologous polypeptide; and (ii) at least a mucocyst-targeting polypeptide of a mucocyst-targeted protein; wherein expression of said first fusion protein results in trafficking of said first fusion protein to mucocysts within said ciliate; and wherein an endogenous protease within said mucocysts cleaves a cleavage site within said mucocyst-targeting polypeptide and removes any sequences C-terminal to said cleavage site, thereby producing a second fusion protein within said mucocysts; (b) stimulating regulated secretion from said mucocysts of said ciliate, whereby an extracellular matrix is formed; and (c) separating said heterologous polypeptide from said extracellular matrix and said ciliates. (a) transforming said ciliate with a nucleic acid encoding a first fusion protein comprising from N-terminus to C-terminus: (i) a heterologous polypeptide; and (ii) at least a mucocyst-targeting polypeptide of a mucocyst-targeted protein; wherein expression of said first fusion protein results in trafficking of said first fusion protein to mucocysts within said ciliate; and wherein an endogenous protease within said mucocysts cleaves a cleavage site within said mucocyst-targeting polypeptide and removes any sequences C-terminal to said cleavage site, thereby producing a second fusion protein within said mucocysts; (i) a heterologous polypeptide; and (ii) at least a mucocyst-targeting polypeptide of a mucocyst-targeted protein; (b) stimulating regulated secretion from said mucocysts of said ciliate, whereby an extracellular matrix is formed; and (c) separating said heterologous polypeptide from said extracellular matrix and said ciliates.