Characteristics and clustering of human ribosomal protein genes.
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.


CONCLUSIONS
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.
Ishii
Kyota
K
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan. kyota@sfc.keio.ac.jp
Washio
Takanori
T
Uechi
Tamayo
T
Yoshihama
Maki
M
Kenmochi
Naoya
N
Tomita
Masaru
M
D000596:Amino Acids / Q000235:genetics; D000818:Animals; D001665:Binding Sites; D003062:Codon / Q000235:genetics; D017124:Conserved Sequence; D020869:Gene Expression Profiling; D006801:Humans; D051379:Mice; D010750:Phosphoproteins / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012269:Ribosomal Proteins / Q000235:genetics*; D012680:Sensitivity and Specificity; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
D000596:Amino Acids; D003062:Codon; D010750:Phosphoproteins; D012269:Ribosomal Proteins; D014157:Transcription Factors; C031937:phosphoprotein P2, ribosomal; C035690:ribosomal phosphoprotein P1; C054675:ribosomal protein P0; C076844:RPL41 protein, human