Juvenile neuronal ceroid lipofuscinosis (
Batten disease) is a childhood
neurodegenerative disease that is caused by mutations in the CLN3 gene. The
protein encoded by CLN3 has no homology with any
proteins of known function and its cellular role remains elusive. In order to investigate the role played by the CLN3
protein we aimed to identify interacting
proteins. Here, we describe the yeast two-hybrid system as the approach taken to investigate such
protein-
protein interactions. CLN3 was expressed as a fusion
protein with
a DNA-binding domain and used to screen a library of human fetal brain cDNAs fused to a transcriptional activation domain. Owing to low level expression of the full length CLN3 fusion
protein, truncated regions corresponding to the predicted hydrophilic regions were also tested. No
proteins that interact with CLN3 were detected, nor was there any evidence for CLN3-CLN3 interactions. Potential interaction of CLN3 with
subunit c of mitochondrial ATP synthase, the major component of the storage material that accumulates in
Batten disease patients, was also tested. No interaction was detected suggesting that the accumulation of subunit c does not result from loss of a process that requires a direct interaction with CLN3. We conclude that either CLN3 does not interact with other
proteins or such interactions cannot be detected using the two-hybrid system.