RPS4Ygene family evolution in primates
© Andrés et al; licensee BioMed Central Ltd. 2008
Received: 03 December 2007
Accepted: 13 May 2008
Published: 13 May 2008
The RPS4 gene codifies for ribosomal protein S4, a very well-conserved protein present in all kingdoms. In primates, RPS4 is codified by two functional genes located on both sex chromosomes: the RPS4X and RPS4Y genes. In humans, RPS4Y is duplicated and the Y chromosome therefore carries a third functional paralog: RPS4Y2, which presents a testis-specific expression pattern.
DNA sequence analysis of the intronic and cDNA regions of RPS4Y genes from species covering the entire primate phylogeny showed that the duplication event leading to the second Y-linked copy occurred after the divergence of New World monkeys, about 35 million years ago. Maximum likelihood analyses of the synonymous and non-synonymous substitutions revealed that positive selection was acting on RPS4Y2 gene in the human lineage, which represents the first evidence of positive selection on a ribosomal protein gene. Putative positive amino acid replacements affected the three domains of the protein: one of these changes is located in the KOW protein domain and affects the unique invariable position of this motif, and might thus have a dramatic effect on the protein function.
Here, we shed new light on the evolutionary history of RPS4Y gene family, especially on that of RPS4Y2. The results point that the RPS4Y1 gene might be maintained to compensate gene dosage between sexes, while RPS4Y2 might have acquired a new function, at least in the lineage leading to humans.
RPS4 genes encode for the ribosomal protein small subunit 4 (29kD; 263 amino acids), a protein involved in mRNA binding and located at the 40S/60S subunit interface of the small ribosomal subunit . The RPS4 protein is well-conserved in prokaryotes and eukaryotes, which suggests strong functional constraints on structural evolution .
RPS4 is found on autosomes in all vertebrates except mammals, which all have an X-linked copy (RPS4X). Fisher et al.  found a Y-linked copy (RPS4Y) in humans, and Omoe and Endo  postulated that RPS4Y was primate specific. However, this study was performed using only great apes and rodents. Moreover, Jegalian and Page  found a Y-linked copy in a marsupial species, the gray short-tailed opossum (Monodelphis domestica), and Skaletsky et al.  found this gene in the first X-degenerate block suggesting that RPS4Y1 was present before mammalian radiation. Recently, another Y-linked copy has been discovered on the human Y chromosome and has been named RPS4Y2  in order to distinguish it from the first copy, which is now called RPS4Y1. The existence of two paralogous copies is a unique feature of human RPS4 compared to other ribosomal proteins , and the presence of three copies is even more surprising. This characteristic is also present in Pan troglodytes, based on Ensembl information . The maintenance of RPS4Y copies in the genome is unexpected as it would destroy the equimolarity among ribosomal proteins described by Meyuhas et al. . These authors showed that the expression of ribosomal protein genes must be regulated in a coordinated way in order to ensure the correct assembly of the elements of the ribosomal complex.
RPS4Y1 is ubiquitously expressed and it is located in position p11.31 . Watanabe et al.  demonstrated that this gene is functional and functionally interchangeable with RPS4X and, despite the lower expression level of RPS4Y, both copies appeared to be necessary for correct development [10, 11]. Thus, RPS4X and RPS4Y proteins are both found in primate male ribosomes while primate female RPS4X genes escape inactivation. Bergen et al.  found an increased substitution rate in great ape RPS4Y1 than in the X-linked copies, showing fewer functional constraints on the Y genes.
RPS4Y2 shows a testis-specific expression pattern in human lineage [; Rozen, personal communication] and it is located in position q11.223, a region associated with infertility (AZFb). However, nothing is yet known about RPS4Y2 essentiality, or about its functionality, expression pattern in non-human primates, or the mechanisms associated with its survival. It might be possible that RPS4Y2 gene had accumulated mutations that would have improved an extra-ribosomal function already present in the gene since it has been described that ribosomal proteins can perform other functions in addition to their role in the protein synthesis . In fact, Fisher et al.  suggested that haploinsufficiency in RPS4 could contribute to Turner syndrome. This, in turn, led Wool  to postulate that RPS4 could be involved in the regulation of development.
Here we describe the evolutionary history of RPS4Y genes in primates. The study was conducted by analyzing DNA sequences from different species covering the entire primate phylogeny. Our aim was to elucidate the evolutionary mechanisms operating in the retention of these genes and the possible role of positive selection in their evolution. We also estimated the age of the duplication event. Finally, we have discussed the functional implications of RPS4Y2 protein evolution.
Pseudogene sequences were identified in great apes, OWM and NWM, but not in strepsirrhines. These findings suggested that the RPS4Y pseudogene was generated after the divergence of strepsirrhines but before the divergence of NWM. Since NWM presented these sequences, it can be inferred that the pseudogene derived from the ancestral RPS4Y copy.
We conducted a number of relative rate tests to detect putative deviations from the molecular clock expectations. For cDNA sequences, the results suggested that, using RPS4X sequences as the outgroup, only combinations involving pseudogene sequences produced statistically significant results (p-value < 0.04). With respect to intronic concatenated sequences, macaque was the only lineage to generate differences when comparing RPS4Y2 sequences and using NWM sequence as the outgroup (p-value < 0.04). The same results were obtained after the FDR correction for multiple tests (data not shown).
To determine the effect of natural selection on coding gene regions, we applied a number of maximum likelihood codon models implemented in the PAML software package . To control the false discovery rate for multiple tests we applied the method described in .
Parameter estimates for the one ratio and free-ratio branch models.
One ratio (M0)
ω = 0.161
Ggo ω = 1.27
One ratio (M0)
ω = 0.278
One ratio (M0)
ω = 0.0001
Ptr ω = 15.81
One ratio (M0)
ω = 0.192
Ptr Y1 ω = 1.71;
Ggo/Mfu Y1 ω = 1.41
One ratio (M0)
ω = 0.069
Ggo/Mfu ω = 1.30
One ratio (M0)
ω = 0.058
No Hsa Y2
Ggo/Mfu ω = 1.30
One ratio (M0)
ω = 0.1520
No Hsa Y2
Ppa ω = 1.25;
Ggo/Mfu Y1 ω = 1.46
One ratio (M0)
ω = 0.051
Site-specific likelihood models [19, 20] make it possible to detect variable selective pressures across sites. Three nested models were performed: M1 (neutral) and M2 (selection); M0 (one ratio) and M3 (discrete); and M7 (beta) and M8 (beta&ω). None of the LRT tests was significant; we therefore found no evidence for sites evolving under positive selection across the different species.
Parameter estimates for branch-site model A from maximum likelihood analyses.
Positive selection (BEB)
p0 = 1 p1 = 0 (p2+p3 = 0), ω2 = 1
p0 = 0 p1 = 0 (p2+p3 = 1), ω2 = 139.62
68H*, 70L*, 87I*, 108C*, 185A*
p0 = 1 p1 = 0 (p2+p3 = 0), ω2 = 1
p0 = 0 p1 = 0 (p2+p3 = 1), ω2 a
p0 = 0 p1 = 1 (p2+p3 = 1), ω2 = 139.62
p0 = 0 p1 = 0 (p2+p3 = 1), ω2 a
68R*, 70I*, 87M*, 104D*, 108R*, 185G*
p0 = 0.942 p1 = 0.058 (p2+p3 = 0), ω2 = 1
Y1Y2X No Hsa Y2
p0 = 0.939 p1 = 0.061 (p2+p3 = 0), ω2 = 1
Y1Y2 No Hsa Y2
p0 = 0.901 p1 = 0.099 (p2+p3 = 0), ω2 = 1
p0 = 0.647 p1 = 0.021 (p2+p3 = 0.332), ω2 = 1
68R, 70I, 87M, 104D, 108R, 180L, 185G, 205F, 222L (P > 0.71)
Positive positions selected by Bayes Empirical Bayes analysis in model A of the PAML.
Ancestral amino acid
Polarity & Volume
a, b, c
a, b, c
We compared the number of synonymous and non-synonymous substitutions in each human RPS4 gene family branch (FR model, using RPS4X as the ancestral sequence) to determine the putative correlation expected under the neutral model. We did not found significant differences between RPS4Y1 and RPS4Y2 (Fisher exact test, p = 0.54), although the two Y-linked RPS4 copies evolved at different rates than the X copy (p < 0.0005).
Nucleotide divergence of Hsa and Ptr sequences estimated by pairwise comparisons using DnaSP and PAML software.
First efforts to describe mammalian RPS4 phylogeny suggested that RPS4 moved to the X chromosome before mammalian radiation while RPS4 Y-linked copy was primate specific . However, the discovery of a Rps4 Y-linked copy in the non-primate species M. domestica  and the location of human RPS4Y in an X-degenerate block  suggest that RPS4X and RPS4Y were present in the ancestral mammalian sex chromosomes but were lost in the Y-chromosome of most lineages during the mammalian evolution . Here we have demonstrated that species along all primate phylogeny maintained the RPS4Y1 gene and that the second Y-linked copy was originated from the duplication of the RPS4Y1 gene after the divergence of NWM but before the radiation of OWM (Fig. 3 shows a scheme of RPS4 evolution in mammals).
The loss of RPS4Y1 gene in most mammals is a result of the degeneration, in both size and gene content, of the Y-chromosome during evolution. It seems that most of the genes retained are related to male-specific functions . Then, the maintenance of ribosomal proteins in primate Y chromosome is unexpected and the mechanisms operating under their retention are still unknown. Since it has been demonstrated that RPS4Y1 maintains the ribosomal activity and it is essential for viability, a possible explanation for its preservation might be the compensation of gene dosage between sexes. Since genes on the X chromosome are inactivated to overcome sex differences, ribosomal proteins on the X chromosome need a mechanism to achieve equimolarity with other ribosomal proteins. In non-primate mammals, the active RPS4X in females and the sole RPS4X in males therefore need to be more fully expressed than autosomal genes. The existence of a functional Y-linked copy in primates has led RPS4X to escape inactivation, as RPS4Y entails gene dosage compensation. In fact, in humans, the other three ribosomal X chromosome protein genes (RPL10, RPL36A, and RPL39) achieve equimolarity by using functional processed copies (RPL10L, RPL36AL, and RPL39L) elsewhere in the genome . However, this hypothesis could not explain the maintenance of the RPS4Y2 gene.
Gene duplication is a major force for the rise of new gene functions in evolution. The average rate of gene duplication is 0.01 per gene per million years . However, the most common fate of duplicate pairs is that one of the copies becomes a pseudogene by the fixation of deleterious mutations, and will finally be lost in the genome. Half-lives of duplicated genes that finally disappear tend to range from 1 to 17 million years . We have shown that RPS4Y2 emerged in the primate phylogeny between the divergence of NWM and OWM. Despite the fact that the expression pattern of RPS4Y2 in non-human primates is still unknown, the absence of stop codons in the open reading frame suggests that the gene is still active, at least in Mfu and Ptr. We can therefore undoubtedly discard a pseudogenization process since the gene has remained in the genome for approximately 35 million years.
On the other hand, duplicated genes can be retained in the genome after neofunctionalization – when a completely new function is acquired  – or subfunctionalization – when either the two genes become specialized in different tissues or at different developmental stages  or when the ancestral gene had several functions and the duplicates become specialized for certain of these functions. It has been found that positive selection plays an important role in duplicated gene retention in mammalian genomes  and is active in both events. The testis and prostate-specific expression found in human RPS4Y2 points to a subfunctionalization event. This hypothesis is supported by the fact that the human RPS4Y2 promoter presents the oligopyrimidine tract as being disrupted by a mutation (data not shown). This tract is the only feature present in all ubiquitously expressed human ribosomal proteins  and its disruption would account for the specificity of RPS4Y2 expression in humans. Interestingly, the oligopyrimidine tract of the promoter in chimpanzee RPS4Y2 has remained untouched, which would suggest ubiquitous expression in this species. Studies of RPS4Y2 expression patterns in all primate lineages are needed to elucidate whether this expression is testis-specific as in humans or ubiquitous as suggested by our observations relating to the chimpanzee RPS4Y2 promoter. If human-specific testis restricted expression is confirmed, RPS4Y2 would compile all the characteristics mainly associated with human speciation – testis-specific expression and human-specific expression pattern and function .
However, the detection of positive selection and the relaxation of purifying selection suggest that RPS4Y2 copy has either undergone a neofunctionalization process or been subjected to a functional specialization, at least in the human lineage. We found that model A (test 1) pointed to six positively-selected positions, while test 2, which is more powerful, but very conservative, confirmed positive selection in only two of the amino acid positions. Since current statistical methods are very conservative at the moment of detecting weak positive selection, some of the other positions identified by test 1 may also have been affected by positive selection.
It is not clear which specific activity of RPS4Y2 could be affected since the six positively-selected amino acids involve all of the protein domains. There were three amino acids in the S4 domain (amino acids 68, 70, 87), two in the ribosomal_S4E domain (104, 108), and one in the KOW domain (185). All changes in the S4 domain were conservative, while changes in the ribosomal_S4E and KOW domains were radical. Moreover, the amino acid affected by positive selection in the KOW domain of RPS4Y2 is the only residue conserved in the KOW motif – a glycine in position 11 – . In human RPS4Y2, this invariable glycine residue has been replaced by an arginine, and so the function of the domain may be dramatically affected. Mutations in human RPS4Y2 gene, therefore, may have improved an extra-ribosomal function that was already present in the ancestral gene. On the other hand, RPS4Y2 location in the azoospermia region AZFb – where large microdeletions have been described to cause azoospermia, even if the genes responsible for this phenotype have not yet been identified  – and its testis-specific expression pattern point to a possible connection between RPS4Y2 and fertility. These features suggest that RPS4Y2 may have acquired a new spermatogenesis-related function in human male lineage; this would be consistent with the observed excess of sperm-specific genes affected by positive selection . In order to elucidate the putative effects of the amino acid changes on the protein function, its interactions within the ribosomal complex, and the binding to RNA, it is necessary to carry out further functional and biochemical studies. It is especially interesting to elucidate if RPS4Y2 maintains the ribosomal protein function. If so, this is the first time that positive selection acting on ribosomal protein is unambiguously demonstrated. Only one recent study  suggested that three ribosomal protein genes (one in the human genome and two in the chimpanzee genome) might be positively selected, but signs of positive selection were weak and it was not possible to distinguish between positive selection and a relaxation of selective constraints. Complementation analyses of a rodent Rps4 knockout mutant with human RPS4Y2 gene would help to elucidate if this gene still conserves its original function or whether, according to the evidences presented in this work, it has acquired a functional specialization related to an extra-ribosomal function or even a new function. Moreover, studies to correlate testis histopathology with different combinations of loss of genes located in AZF regions would reveal if RPS4Y2 has acquired a fertility-related function.
In conclusion, using comparative sequence analyses, we were able to establish the genealogy of RPS4Y genes in primate phylogeny, corroborating the preservation of the first RPS4Y gene in all primate infraorders and dating the origin of RPS4Y2 as occurring between the divergence of NWM and OWM. RPS4Y1 maintenance seems to be the result of a mechanism for compensating gene dosage between sexes. On the other hand, we detected that the human RPS4Y2 gene evolved under positive selection. The results and evidences presented here point to the acquisition of a non-ribosomal function -an extra-ribosomal or a completely new male-specific function- of the RPS4Y2 in the human lineage.
Samples of Homo sapiens (Hsp), great apes -Pan troglodytes (Ptr), Gorilla gorilla (Ggo), and Pongo pygmaeus (Ppy) -, Old World monkeys (OWM) -Macaca fuscata (Mfu), and Mandrillus sphinx (Msp) -, New World monkeys (NWM) -Saimiri boliviensis (Sbo), Callithrix jacchus (Cja), and Callicebus moloch (Cmo) -, and strepsirrhines -Eulemur fulvus (Efu), and Eulemur macaco (Ema)- were provided from the INPRIMAT sample collection. For tissue and blood samples DNA was extracted using the Qiagen tissue kit (Qiagen, Valencia, CA, USA) following the manufacturer's instructions. Initial amounts were 25 mg for muscle tissues and 100 μl for blood samples. DNA from cell lines was also provided by INPRIMAT DNA collection (see Additional file 2).
Amplification and sequencing
Intron 3 and intron 6 of RPS4Y genes were found suitable for amplification, since they allowed the location of both forward and reverse primers on exonic sequences to amplify the full intron (Fig. 1). Primers were designed to be male specific and to distinguish between RPS4Y2 and RPS4Y1 in different primate species. We also designed another pair of primers to amplify a complete 7-exon mRNA RPS4Y pseudogene (Fig. 1). The names and sequences of the oligonucleotides are shown in Additional file 3. We have described the PCR conditions, fragments resulting from the use of different primer combinations, and species specificity in Additional file 4.
PCR products were purified using the GFX PCR DNA and Gel Band Purification Kit (Amersham Biosciences UK Limited, Buckinghamshire, UK). Both strands were sequenced from the purified products using forward and reverse PCR primers (sequencing conditions are described in Additional file 4).
Genomic sequences and information concerning human and chimpanzee RPS4 genes were taken from Ensembl . We used the RepeatMasker v3.1.6. program  to detect interspersed repeats in Ensembl genomic sequences.
We handled DNA sequences from this study and protein and cDNA sequences obtained from GenBank (see Additional files 5 and 6 for accession numbers) with BioEdit v6.0.7 . Multiple alignments were obtained by Clustal W  or DiAlign2  and subsequently manually edited to minimize the number of gaps.
Once aligned, we applied Gblocks  to eliminate poorly aligned positions and divergent regions of our intronic sequences in order to obtain reliable blocks that were suitable for phylogenetic analysis. We used DnaSP v4.0  to estimate nucleotide diversity and descriptive statistics to examine the different sequence sets.
For each alignment, we selected the nucleotide substitution model that best fitted the data among 56 different evolutionary models based on the Akaike Information Criteria approach using Modeltest 3.6 . We constructed a phylogenetic tree (Fig. 2) based on the neighbor-joining (NJ) method , using PAUP*v4.0b10 . Confidence in the resulting relationships was assessed using 10,000 bootstrap replicates . We also performed relative rate tests on the trees by applying the RRTree program , which compares substitution rates between lineages of DNA sequences, relative to a particular outgroup. TreeView  was used to visualize trees.
Analysis of the impact of positive or negative selection on DNA coding region was conducted using Phylogenetic Analysis by Maximum Likelihood (PAML) v3.12  and DnaSP  software. We applied the different codon substitution models implemented in codeml (Branch Models, Site Models and Branch-Site Models). We applied a FDR correction for multiple tests in all analyses.
We estimated the time of the duplication event (Td) from the mean number of synonymous substitutions per site () among all paralogous combinations. For each paralogous copy, the synonymous substitution rate (r) was estimated for all possible pairs of species, as r = Ks/2*Ts, where Ks is the number of synonymous substitutions per site and Ts is the divergence time for each pair of species. For Ts, we took the minimum and maximum values from Goodman et al. . Average rates (ř) for both the minimum and maximum values were obtained from the slope of a regression analysis. We then applied the equation Td = /2*ř to find the estimated duplication time range.
This paper is dedicated to the memory of Xavier Domingo-Roura. We would like to thank M. Rocchi for his help with the FISH analyses. Financial support was provided by the European Commission under contract QLRI-CT-2002-01325 (INPRIMAT project). O. Andrés was supported by scholarships from the DURSI, Generalitat de Catalunya (Ref. 2003FI-00787) and T. Kellermann was supported by a scholarship from the German Academic Exchange Service (DAAD). We would also like to thank the INPRIMAT Consortium http://www.inprimat.org for supplying the samples.
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