Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes

Abstract

We have identified a new class of ribosomal protein (RP) genes that appear to have been retrotransposed from X-linked RP genes. Mammalian ribosomes are composed of four RNA species and 79 different proteins. Unlike RNA constituents, each protein is typically encoded by a single intron- containing gene. Here we describe functional autosomal copies of the X-linked human RP genes, which we designated RPL10L (ribosomal protein L10-like gene), RPL36AL and RPL39L after their progenitors. Because these genes lack introns in their coding regions, they were likely retrotransposed from X-linked genes. The identities between the retrotransposed genes and the original X-linked genes are 89-95% in their nucleotide sequences and 92-99% in their amino acid sequences, respectively. Northern blot and PCR analyses revealed that RPL10L and RPL39L are expressed only in testis, whereas RPL36AL is ubiquitously expressed. Although the role of the autosomal RP genes remains unclear, they may have evolved to compensate for the reduced dosage of X-linked RP genes.

Figure 1

Structure of autosomal RP genes. Intron/exon structures were compared with those of the original X-linked genes. The GC content was calculated by GENETYX as an average of 200 bp windows in every 20 bp step. Boxes indicate exons and horizontal lines indicate introns or flanking regions. Coding regions are blackened in the X-linked genes and are shaded in the autosomal genes.

Figure 2

Chromosomal mapping of autosomal RP genes. RPL39L was mapped to chromosome 3, and RPL10L and RPL36AL were mapped to chromosome 14 using radiation hybrid panels. They are shown in relation to nearby markers and the approximate distance (in centiMorgans and centiRays) from the most distal short-arm marker on the STS content map (http://www-genome.wi.mit.edu/cgi-bin/contig/phys-map). Locations of the X-linked RP genes and RPS4Y are also shown.

Figure 3

Northern blot analysis of X-linked and retrotransposed genes. Two types of human MTN blots were hybridized with ³²P-labeled probes synthesized from the 3′-non-coding region of the genes.

Figure 4

Expression analysis of X-linked and retrotransposed genes by PCR. The human MTC panels, including 16 normal tissues (lanes 1–16) and 8 tumor cell lines (lanes 17–24) were typed by PCR using the primers listed in Table 1. Lane M, 100 bp ladder size marker; car, carcinoma; ad, adenocarcinoma.

Figure 5

Alignment of the 5′-non-coding regions of retrotransposed genes. Identical bases between the genes are shaded. Gaps (hyphens) are inserted to optimize alignment. The numbers appearing above the RP gene sequences represent the nucleotide position from the translation initiator ATG codon. A sequence of 43 bp from the U3 region of HERV-K LTR is also aligned. Positions according to the complete HERV-K sequence (accession no. AF074086) are shown in parentheses.