We have identified functional homologs of human X-linked RP genes and have localized them to autosomes. Because these genes have no introns in their coding regions, they were most likely produced by retrotransposition of the original X-linked genes during evolution. Although each mammalian RP is typically encoded by a single gene, this functional gene also generates a large number of retroposons. However, the majority of these retroposons would not be expected to survive during evolution because, without promoters, they are inactive at integration sites and would therefore accumulate mutations in their open reading frames. In fact, there are at least a dozen processed pseudogenes for each RP gene in the genome (28
). In this study we have identified three genes that appear to have been protected from such evolutionary pressure and to be actively transcribed. Similar retrotransposed genes have been reported, including PGK2
and HNRNP G-T
). All of these genes have a progenitor on the X chromosome and are highly expressed in testis. We also observed testis-specific expression of RPL10L
, which may indicate a role of the retrotransposed genes in compensating for the inactivated X-linked genes during spermatogenesis.
Based on their findings, which included an analysis of 49 intronless paralogs of autosomal RP genes, Venter et al
) suggested that there was no bias toward the X chromosome origination of active retroposons during evolution. Because we have identified only three active RP retroposons despite a thorough search of the public DNA databases and have found that all of these genes originated from the X chromosome, we believe that there may actually have been a strong bias for retrotransposition of X chromosome RP genes.
Haploinsufficiency of any of the RP genes causes viable but abnormal phenotypes (Minute
) in Drosophila
), and heterozygous mutations in RPS19
are associated with DBA (13
), suggesting that two copies of each RP gene are essential for normal growth and development. It therefore seems that genes on the sex chromosomes must increase their expression levels to compensate for gene dosage. One of these genes, RPS4X
, reportedly escapes X-inactivation, and both it and its Y homolog (RPS4Y
) are ubiquitously expressed (15
). In contrast, we have shown in this study that the remaining X-linked RP genes have autosomal copies, which are expressed either ubiquitously or only in testis. Recently, we have reported a unique feature of RP gene promoters in which transcription always starts within a characteristic oligopyrimidine tract (34
). We found this oligopyrimidine tract in the 5′-upstream region of RPL36AL
, which is expressed ubiquitously, but not in those of RPL10L
, which are expressed only in testis (data not shown). This oligopyrimidine tract may therefore play an important role in ubiquitous RP gene expression.
Several mechanisms have been proposed for retroposons to acquire a functional promoter (35
). For example, (i) the retroposon may contain the original gene promoter, (ii) the insertion may occur near an existing promoter, and (iii) mutations may create a functional promoter upstream of the retroposon insertion. The three retroposons identified in this study have little similarity to the original X-linked genes in their 5′-non-coding regions but are slightly similar to HERV-K LTR in a small 70 bp region. A large number of solitary HERV LTRs have been created by homologous recombination, and their possible role in promoter control of downstream genes has been proposed (38
). We also found such similarity in previously reported X-originated retroposons, including PGK2
and HNRNP G-T
(data not shown). Also, Chen et al
. found the similarity in the 5′-non-coding region of mouse zinc-finger protein Zfp352
gene, which is thought to have arisen from retrotransposition (40
). HERV-K LTR, therefore, might be involved in the active transcription of these retrotransposed genes.
Finally, we searched the DNA databases for mouse RP orthologs, and found three genes, designated Rpl10l, Rpl36al and Rpl39l, which correspond to human RPL10L, RPL36AL and RPL39L, respectively (data not shown). They are 84–92% similar to the human genes in their nucleotide sequences and are located in the syntenic regions between the two species. Moreover, the EST database search has shown that Rpl36al is expressed ubiquitously, whereas Rpl10l and Rpl39l are expressed primarily in testis, which is consistent with the human gene expression patterns. Further experiments using the mouse system will be of great interest to understand the function of these retroposons.