Nuclear proteins with charge periodicity of 28 residues are specifically increased in vertebrate genomes

Abstract

More than 36,000 open reading frames (ORFs) from the human genome were previously analyzed by the autocorrelation function of electric charge distribution, revealing the existence of many proteins with a charge periodicity of 28 residues (PCP28) (Ke et al., Jpn. J. Appl. Phys. 2007). The major component of PCP28 was located in the nucleus, and the nuclear PCP28 of ten vertebrate and seven invertebrate organisms were predicted with a novel software system (Sakiyama et al., CBI Journal 2007) for revealing the biological significance of nuclear PCP28. Retrieval of the features of the human nuclear PCP28 in Swiss-Prot revealed that almost 90% of nuclear PCP28 functions in transcriptional regulation, including hypothetical transcription factors. To study how nuclear PCP28 is increased in eukaryote genomes, we compared the number of all nuclear PCP28 in vertebrate and invertebrate genomes. The results showed that nuclear PCP28 is specifically increased in vertebrate genomes and that the ratio of other types of PCP28 is almost constant in all eukaryote genomes. These findings strongly suggest that nuclear PCP28 is an essential protein for vertebrate organisms.