Origin and evolution of processed pseudogenes that stabilize functional Makorin1 mRNAs in mice, primates and other mammals - PubMed (original) (raw)
Origin and evolution of processed pseudogenes that stabilize functional Makorin1 mRNAs in mice, primates and other mammals
Satoko Kaneko et al. Genetics. 2006 Apr.
Abstract
We investigate the origin and evolution of a mouse processed pseudogene, Makorin1-p1, whose transcripts stabilize functional Makorin1 mRNAs. It is shown that Makorin1-p1 originated almost immediately before the musculus and cervicolor species groups diverged from each other some 4 million years ago and that the Makorin1-p1 orthologs in various Mus species are transcribed. However, Mus caroli in the cervicolor species group expresses not only Makorin1-p1, but also another older Makorin1-derived processed pseudogene, demonstrating the rapid generation and turnover in subgenus Mus. Under this circumstance, transcribed processed pseudogenes (TPPs) of Makorin1 evolved in a strictly neutral fashion even with an enhanced substitution rate at CpG dinucleotide sites. Next, we extend our analyses to rats and other mammals. It is shown that although these species also possess their own Makorin1-derived TPPs, they occur rather infrequently in simian primates. Under this circumstance, it is hypothesized that already existing TPPs must be prevented from accumulating detrimental mutations by negative selection. This hypothesis is substantiated by the presence of two rather old TPPs, MKRNP1 and MKRN4, in humans and New World monkeys. The evolutionary rate and pattern of Makorin1-derived processed pseudogenes depend heavily on how frequently they are disseminated in the genome.
Figures
Figure 1.
The NJ trees for the B region (A) and the C region (B) of Makorin1 and its processed pseudogenes in mice. The sequences in P
odlaha
and Z
hang
(2004) are boxed. Both _p_-distance-based trees are rooted by Rano Mkrn1. The B and C regions compared are 609 and 581 bp long, respectively. Regarding Muca Mkrn1, the B region is taken from the NCBI database (AH014504), whereas the C region sequence determined here is 342 bp long and excluded in B. The number near each node represents the bootstrap value in 10,000 resamplings, but <50% bootstrap values are suppressed. The bar at the bottom shows the number of nucleotide differences per site. The abbreviations of the genus and species names are: Mudo (Mus m. domesticus), Mumu (Mus m. musculus), Mucs (Mus m. castaneus), Mumo (Mus m. molossinus), Musp (Mus spretus), Muca (Mus caroli), and Rano (Rattus norvegicus).
Figure 2.
The scatter diagram of the _p_-distances between the B and C regions in the pairwise comparison of the Mkrn1-p1 orthologs. Solid circles show the comparisons based on our sequences, whereas open triangles show those based on P
odlaha
and Z
hang
(2004). The conserved pattern of the B region in the latter comparisons is largely attributed to the dubious sequences of M. caroli and M. cervicolor.
Figure 3.
The _p_-distance-based NJ trees for Mkrn1 and its processed pseudogenes in mice and rats. The tree is rooted by Hosa MKRN1. The MP tree is topologically the same as the NJ tree. The number of sites in this comparison is 931 bp. The number close to each node represents the bootstrap value in 10,000 resamplings. The scale bar is given at the bottom. The abbreviations of the genus and species names are the same as those in Figure 1.
Figure 4.
Restriction enzyme analyses of transcripts of Mkrn1 and its processed pseudogenes in Mus and Rattus. The RT–PCR products were digested by _Hin_dIII, _Eco_RI, or _Bgl_II and separated by electrophoresis on a 1.5% agarose gel. (Lanes a and b) In M. m. domesticus and M. spretus (SPRET/Ei), there is a _Hin_dIII site in Mkrn1, but not in Mkrn1-p1. (Lane c) In M. caroli, a _Hin_dIII site is present in Mkrn1-p1.a, but absent in Mkrn1-p1.b, Mkrn1, and Mkrn1-p2. (Lane d) In M. caroli, an _Eco_RI site is present in Mkrn1-p1.a/b and Mkrn1, but absent in Mkrn1-p2. (Lane f) In R. norvegicus, Mkrnp1 has a _Bgl_II site, but Mkrn1 does not. Lanes e and g represent negative controls in M. caroli and R. norvegicus, respectively. These control experiments were carried out using total RNA to confirm no contamination of genomic DNA in samples. The molecular weight standards are shown on the left- and rightmost lanes (M1 and M2).
Figure 5.
The NJ tree of Makorin1 and its processed pseudogenes in primates and other mammals. The tree is based on the _p_-distances over 655 bp under complete deletion. The number close to each node represents the bootstrap value (≥50%) in 10,000 resamplings. The scale bar is represented at the bottom. The abbreviations of the genus and species names are: Hosa (Homo sapiens), Patr (Pan troglodytes), Saoe (Saguinus oedipus), Aotr (Aotus trivirgatus), Atbe (Ateles belzebuth), Ceap (Cebus apella), Gamo (Galago moholi), Otcr (Otolemur crassicaudatus), Gade (Galagoides demidoff), Cafa (Canis familiaris), Bota (Bos taurus), Rano (Rattus norvegicus), and Maeu (Macropus eugenii).
Figure 6.
The ratio (γ) of the _p_-distances in the B region to those in the C region in orthologous pairs of _MKRN1_-derived processed pseudogenes in simian primates (ordinate) and the _p_-distances in the C region of these processed pseudogenes measured from Hosa MKRN1 (abscissa). As in Figure 5, there are 16 such pairs, of which 6 are for MKRNP1 (open triangles); 6 are for MKRNP4 (open squares); and 1 each is for MKRN4, MKRN5, MKRNP3, and MKRNP7. These last four comparisons are indicated by solid diamonds, but distinguished by different numbers. The six comparisons of MKRNP1 or MKRNP4 are divided into two according to the _p_-distances on the abscissa. These four trios are indicated by Atbe P1 and Ceap P1 or Aotr P4 and Saoe P4. The lowest γ-value among the _MKRNP1_s is realized by the comparison between the human and the chimpanzee.
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