Characteristics and clustering of human ribosomal protein genes

Kyota Ishii¹^,2 , Takanori Washio¹^,3 , Tamayo Uechi⁴ , Maki Yoshihama⁴ , Naoya Kenmochi⁴ and Masaru Tomita¹^,5

¹Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan

²Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan

³Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan

⁴Frontier Science Research Center, University of Miyazaki, Kiyotake, Miyazaki 889-1692, Japan

⁵Department of Environmental Information, Keio University, Fujisawa, Kanagawa 252-8520, Japan

author email corresponding author email

BMC Genomics 2006, 7:37doi:10.1186/1471-2164-7-37


Published:	28 February 2006

Abstract

Background

The ribosome is a central player in the translation system, which in mammals consists of four RNA species and 79 ribosomal proteins (RPs). The control mechanisms of gene expression and the functions of RPs are believed to be identical. Most RP genes have common promoters and were therefore assumed to have a unified gene expression control mechanism.

Results

We systematically analyzed the homogeneity and heterogeneity of RP genes on the basis of their expression profiles, promoter structures, encoded amino acid compositions, and codon compositions. The results revealed that (1) most RP genes are coordinately expressed at the mRNA level, with higher signals in the spleen, lymph node dissection (LND), and fetal brain. However, 17 genes, including the P protein genes (RPLP0, RPLP1, RPLP2), are expressed in a tissue-specific manner. (2) Most promoters have GC boxes and possible binding sites for nuclear respiratory factor 2, Yin and Yang 1, and/or activator protein 1. However, they do not have canonical TATA boxes. (3) Analysis of the amino acid composition of the encoded proteins indicated a high lysine and arginine content. (4) The major RP genes exhibit a characteristic synonymous codon composition with high rates of G or C in the third-codon position and a high content of AAG, CAG, ATC, GAG, CAC, and CTG.

Conclusion

Eleven of the RP genes are still identified as being unique and did not exhibit at least some of the above characteristics, indicating that they may have unknown functions not present in other RP genes. Furthermore, we found sequences conserved between human and mouse genes around the transcription start sites and in the intronic regions. This study suggests certain overall trends and characteristic features of human RP genes.