A review of the proteinaceous machinery involved in protein sorting pa
thways and protein folding and assembly in mitochondria and peroxisome
s is presented. After considering the various sorting pathways and tar
geting signals of mitochondrial and peroxisomal proteins, we make a co
mparative dissection of the protein factors involved in: i) the stabil
ization of cytosolic precursor proteins in a translocation competent c
onformation; ii) the membrane import apparatus of mitochondria and per
oxisomes; iii) the processing of mitochondrial precursor proteins, and
the eventual processing of certain peroxisomal precursor, in the inte
rior of the organelles; and iv) the requirement of molecular chaperone
s for appropriate folding and assembly of imported proteins in the mat
rix of both organelles. Those aspects of mitochondrial biogenesis that
have developed rapidly during the last few years, such as the require
ment of molecular chaperones, are stressed in order to stimulate furth
er parallel investigations aimed to understand the origin, biochemistr
y, molecular biology and pathology of peroxisomes. In this regard, a b
rief review of findings from our group and others is presented in whic
h the role of the F1-ATPase alpha-subunit is pointed out as a molecula
r chaperone of mitochondria and chloroplasts. In addition, data are pr
esented that could question our previous indication that the immunorea
ctive protein found in the rat liver peroxisomes is due to the presenc
e of the F1-ATPase alpha-subunit.