Parvulin (Par14), a Peptidyl-Prolyl cis-trans Isomerase, Is a Novel rRNA Processing Factor That Evolved in the Metazoan Lineage

doi:10.1074/mcp.M900147-MCP200

Parvulin (Par14), a Peptidyl-Prolyl cis-trans Isomerase, Is a Novel rRNA Processing Factor That Evolved in the Metazoan Lineage*

From the ^aDepartment of Biotechnology, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan,
^dCenter for Information Biology-DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan,
^eIntegrated Proteomics System Project, Pioneer Research on Genome the Frontier, Ministry of Education, Culture, Sports, Science and Technology of Japan, Tokyo 102-0075, Japan,
^gDepartment of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan,
^hDepartment of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachiouji-shi, Tokyo 192-0397, Japan, and
ⁱCore Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan

^j To whom correspondence should be addressed: Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan. Fax: 81-042-367-5709; E-mail: ntakahas{at}cc.tuat.ac.jp.

↵^c Present address: Inst. of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032.
↵^f Present address: Dept. of Bioscience and Bioinformatics, College of Information Science and Engineering, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Japan.

↵^b Both authors contributed equally to this work.

Abstract

Although parvulin (Par14/eukaryotic parvulin homolog), a peptidyl-prolyl cis-trans isomerase, is found associated with the preribosomal ribonucleoprotein (pre-rRNP) complexes, its roles in ribosome biogenesis remain undetermined. In this study, we describe a comprehensive proteomics analysis of the Par14-associated pre-rRNP complexes using LC-MS/MS and a knockdown analysis of Par14. Together with our previous results, we finally identified 115 protein components of the complexes, including 39 ribosomal proteins and 54 potential trans-acting factors whose yeast homologs are found in the pre-rRNP complexes formed at various stages of ribosome biogenesis. We give evidence that, although Par14 exists in both the phosphorylated and unphosphorylated forms in the cell, only the latter form is associated with the pre-40 S and pre-60 S ribosomal complexes. We also show that Par14 co-localizes with the nucleolar protein B23 during the interphase and in the spindle apparatus during mitosis and that actinomycin D treatment results in the exclusion of Par14 from the nucleolus. Finally we demonstrate that knockdown of Par14 mRNA decelerates the processing of pre-rRNA to 18 and 28 S rRNAs. We propose that Par14 is a component of the pre-rRNA complexes and functions as an rRNA processing factor in ribosome biogenesis. As the amino acid sequence of Par14 including that in the amino-terminal pre-rRNP binding region is conserved only in metazoan homologs, we suggest that its roles in ribosome biogenesis have evolved in the metazoan lineage.

Footnotes

↵* This work was supported in part by the Japan Health Science Foundation (H18-Soyaku-Ippan-001) (to N. T.), by research fellowships of the Japan Society for the Promotion of Science (to S. F.-N.), and by the Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan (to K. H.).
↵ The on-line version of this article (available at http://www.mcponline.org) contains supplemental material.
↵¹ The abbreviations used are:

PPIase

peptidyl-prolyl cis-trans isomerase

CyP

cyclophilin

DAPI

4′,6-diamidino-2-phenylindole

Lys-C

lysyl endopeptidase

Par14

parvulin 14

EPVH

eukaryotic parvulin homolog

PMF

peptide mass fingerprinting

pre-rRNP

preribosomal ribonucleoprotein

RP

ribosomal protein

siRNA

small interference RNA

NCBI

National Center for Biotechnology Information
- Received March 17, 2009.