Autoantibodies to mitochondria (AMA, anti-M2) are a serologic hallmark of p
rimary biliary cirrhosis (PBC). These react with three structurally and fun
ctionally related multienzymic complexes, the 2-oxoacid dehydrogenase compl
exes, but chiefly with die E2 subunit of pyruvate dehydrogenase complex (PD
C-E2). Their very dose (95%) and specific association with PBC underpins th
e autoimmune concept of pathogenesis of that disease, notwithstanding sever
al non-congruent features. Detailed studies, including structural analysis
of epitopes, do nor disclose how these autoantibodies originate. Their ubiq
uity in PBC has overshadowed the existence of a second set of relatively PB
C-specific autoantibodies to nuclear antigens for which reactants have been
. cloned and characterized. These include centromeric proteins; proteins of
the nuclear pore complex; nuclear dot proteins, which include Sp-100 and t
he promyelocytic leukemia antigen; and a recently identified autoantigen, S
OX13. Certain of these reactants are DNA-binding proteins with transcriptio
nal regulatory activity Thus serum from individuals with the same clinical
syndrome can have autoimmune reactivity to disparate mitochondrial and nucl
ear constituents in different cellular compartments. Antibody probing of ph
age displayed random peptide libraries, together with epitope scanning usin
g overlapping sequential octameric peptides from the PDC-E2 sequence, showe
d that the discontinuous motifs MH, FV(E) and SIP contributed to a predicte
d conformational antibody epitope in the inner lipoyl domain of PDC-E2.