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Journal of Biochemistry 2005 138(6):673-678; doi:10.1093/jb/mvi169
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© 2005 The Japanese Biochemical Society.

Regular Paper

PDIP38 Associates with Proteins Constituting the Mitochondrial DNA Nucleoid

Xiaoli Cheng1,2, Tomotake Kanki1, Atsushi Fukuoh1, Kippei Ohgaki1, Ryu Takeya3, Yoshimasa Aoki1, Naotaka Hamasaki1 and Dongchon Kang1,*

1 Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582; 2 Basic Medical College, Zhengzhou University, Henan, China; and 3 Department of Biochemistry and Biotechnology, Kyushu University, Fukuoka 812-8582

* To whom correspondence should be addressed. Tel: +81-92-642-5749, Fax: +81-92-642-5772, E-mail: kang{at}mailserver.med.kyushu-u.ac.jp

Human mitochondrial DNA takes on a large protein-DNA complex called a nucleoid or mitochromosome. Mitochondrial transcription factor A (TFAM) is a major component of the complex. During an attempt to search for proteins associated with the TFAM-containing complex by a proteomic method, we found one protein that has not been considered to be mitochondrial: PDIP38. PDIP38 was initially identified as a binding protein to nuclear DNA polymerase {delta}. PDIP38 is almost exclusively recovered from the mitochondrial fraction of human HeLa cells. PDIP38 is completely cleaved when TritonX-100–solubilized mitochondria are treated with proteinase K, but not when mitoplasts devoid of outer membranes are treated, indicating that PDIP38 is located in the mitochondrial matrix. TFAM and mitochondrial single-stranded DNA binding protein (mtSSB) are co-immunoprecipitated with PDIP38 by anti-PDIP38 antibodies. On the other hand, only the latter is crosslinked to PDIP38 when mitochondria are treated with a crosslinker, formaldehyde. In addition to mtSSB, 60 kDa heat shock protein and a Lon protease homolog, both of which have single-stranded DNA binding activity, are also crosslinked. PDIP38 associates with the nucleoid components and could be involved in the metabolism of mitochondrial DNA.


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