Evolution of RH genes in hominoids: characterization of a gorilla RHCE-like gene

The human RH locus is responsible for the expression of the Rh blood group antigens. It consists of two closely linked genes, RHD and RHCE, that exhibit 92% similarity between coding regions. These observations suggest that they are derived from a relatively recent duplication event. Previously a study of nonhuman primate RH-like genes demonstrated that ancestral RH gene duplication occurred in the common ancestor of man, chimpanzees and gorillas. By amplification of intron 3 and intron 4 of gorilla RH-like genes, we have now shown that, like man, gorillas possess two types of RH intron 3 (RHCE intron 3 being 289 bp longer than the RHD intron 3) and two types of intron 4 (RHCE intron 4 being 654 bp longer than the RHD intron 4). Here we report the characterization of a cDNA encoded by a gorilla RH-like gene which possesses introns 3 and 4 of the RHCE type. A comparison of this gorilla RHCE-like coding sequence with previously characterized human and ape cDNA sequences suggests that RH genes experienced complex recombination events after duplication in the common ancestor of humans, chimpanzees and gorillas.     

Concerted evolution of alpha satellite DNA: Evidence for species specificity and a general lack of sequence conservation among alphoid sequences of higher primates

We investigated relationships among alpha satellite DNA families in the human, gorilla, chimpanzee, and orangutan genomes by filter hybridization with cloned probes which correspond to chromosome-specific alpha satellite DNAs from at least 12 different human chromosomes. These include representatives of both the dimer-based and pentamer-based subfamilies, the two major subfamilies of human alpha satellite. In addition, we evaluated several high-copy dimer-based probes isolated from gorilla genomic DNA. Under low stringency conditions, all human probes tested hybridized extensively with gorilla and chimpanzee alpha satellite sequences. However, only pentameric and other non-dimeric human alphoid probes hybridized with orangutan alpha satellite sequences; probes belonging to the dimer subfamily did not cross-hybridize detectably with orangutan DNA. Moreover, under high stringency conditions, each of the human probes hybridized extensively only with human genomic DNA; none of the probes cross-hybridized effectively with other primate DNAs. Dimer-based gorilla alpha satellite probes hybridized with human and chimpanzee, but not orangutan, sequences under low stringency hybridization conditions, yet were specific for gorilla DNA under high stringency conditions. These results indicate that the alpha satellite DNA family has evolved in a concerted manner, such that considerable sequence divergence is now evident among the alphoid sequences of closely related primate species.     

Structure of the gorilla alpha-fetoprotein gene and the divergence of primates.

The sequence of the gorilla alpha-fetoprotein gene, including 869 base pairs of the 5' flanking region and 4892 base pairs of the 3' flanking region (24,607 in total), was determined from two overlapping lambda phage clones. The sequence extends 18,846 base pairs from the Cap site to the polyadenylation site, and it reveals that the gene is composed of 15 exons, which are symmetrically placed within three domains of alpha-fetoprotein. The deduced polypeptide chain is composed of a 19-amino-acid leader peptide, followed by 590 amino acids of the mature protein. The RNA polymerase II binding site, TATAAAA, and the promoter element, CCAAC, are positioned at -21 and -65 from the Cap site, respectively. The polyadenylation signal, AATAAA, is located in the last exon, which is untranslated. The sequence for the gorilla alpha-fetoprotein gene was compared with that of the previously published human alpha-fetoprotein gene (P. E. M. Gibbs, R. Zielinski, C. Boyd, and A. Dugaiczyk, 1987, Biochemistry 26: 1332-1343). Four types of repetitive sequence elements were found in identical positions in both species. However, one Alu and one Xba DNA repeat within introns 4 and 7, respectively, of the human gene are absent from orthologous positions in the gorilla. The Alu and the Xba DNA repeats probably emerged in the human genome after the human/gorilla divergence and became established novelties in the human lineage. There are 363/21,523 mutational changes between human and gorilla, amounting to 1.69% DNA divergence between the two primate species. The value of 1.69% is lower than the 2.27% obtained from melting temperatures of hybrids between human and gorilla genomic DNA (C. G. Sibley and J. E. Ahlquist, 1984, J. Mol. Evol. 26: 99-121). At the protein level, Homo sapiens differs from Gorilla gorilla only at 4 of 609 amino acid positions (0.66%) in the alpha-fetoprotein sequence. This difference signifies a lower rate of molecular divergence for the alpha-fetoprotein gene in primates, as compared to rodents.     

Focusing on comparative ape population genetics in the post-genomic age

The initial human and chimpanzee genome sequences have been published, and additional primate genomes, including those of gorilla and orang-utan, are in progress. With these new resources, we can now address what makes our species unique, by focusing on the underlying genetic differences associated with phenotypes. Comparative primate population genomics, including studies of structural changes, mobile elements, gene expression and functional analyses, will shed light on how natural selection and population demography are involved in the processes that lead to differences among great apes. Historically, this research has focused on the human perspective; however, we will learn much about ourselves with a focus on genomic diversity in hominoids as a group.     

Perception of stimuli presented as photographic slides in cynomolgus macaques (Macaca fascicularis)

The present study was designed to assess a monkey's perception of specific visual stimuli by measuring both the behavioral responses and duration of attention to the presentation of photographic slides. Five adult male cynomolgus macaques (Macaca fascicularis) were placed individually in an open field apparatus and presented a series of slides consisting of apples, a gorilla mask, a collage of colors, a human being, and a plain field. The slide of the gorilla mask followed by that of the human being received the most attention while the plain field received the least. In addition, the gorilla mask and human being elicited a range of behavioral responses with the higher ranking animals displaying a greater number of aggressive responses and the lower ranking animals displaying a greater number of submissive gestures. Taken together, these data would suggest that the slides of the gorilla mask and the human being were perceived by the monkeys as threatening. These results are consistent with a continuing theme observed among a number of studies of primate social perception — namely, that potentially threatening stimuli are a significant determinant of visual observing.     

Sequence diversification and exon inactivation in the glycophorin A gene family from chimpanzee to human

In humans, the allelic diversity of MNSs glycophorins (GP) occurs mainly through the recombinational modulation of silent exons (pseudoexons) in duplicated genes. To address the origin of such a mechanism, structures of GPA, GPB, and GPE were determined in chimpanzee, the only higher primate known to have achieved a three-gene framework as in humans. Pairwise comparison of the chimpanzee and human genes revealed a high degree of sequence identity and similar exon-intron organization. However, the chimpanzee GPA gene lacks a completely formed M- or N-defining sequence as well as a consensus sequence for the Asn-linked glycosylation. In the case of the GPB gene, exon III is expressed in the chimpanzee but silenced, as a pseudoexon, in the human. Therefore, the protein product in the chimpanzee bears a larger extracellular domain than in the human. For the GPE genes, exon III and exon IV have been inactivated by identical donor splice-site mutations in the two species. Nevertheless, the chimpanzee GPE-like mRNA appeared to be transcribed from a GPB/E composite gene containing no 24-bp insertion sequence in exon V for the transmembrane domain. These results suggest a divergent processing of exonic units from chimpanzee to human in which the inactivation of GPB exon III preserved a limited sequence repertoire for diversification of human glycophorins.Correspondence to: O.O. Blumenfeld     

Synteny comparison between apes and human using fine-mapping of the genome

Comparing the genomes of the great apes and human should provide novel information concerning the origins of humankind. Relative to the great apes, the human karyotype has one fewer chromosome pair, as human chromosome 2 derived from the telomeric fusion of two ancestral primate chromosomes. To identify the genomic rearrangements that accompanied human speciation, we initiated a comparative study between human, chimpanzee, and gorilla. Using the HAPPY mapping method, an acellular adaptation of the radiation hybrid method, we mapped a few hundred markers on the human, chimpanzee, and gorilla genomes. This allowed us to identify several chromosome rearrangements, in particular a pericentric inversion and a translocation. We precisely localized the synteny breakpoint that led to the formation of human chromosome 2. This breakpoint was confirmed by FISH mapping.     

Differences in cell division and thymidine incorporation with rat and primate fibroblasts in collagen lattices.

Human and gorilla dermal fibroblasts, primate cells, suspended in a collagen lattice, do not divide for the first 3 days. In contrast, rat fibroblasts divide within 24 hr. In this study, the proliferation of rat fibroblasts were compared to primate fibroblasts. Rat fibroblasts in monolayer culture increase from 100,000 to 355,000 in 2 days, and human cells increase from 100,000 to 436,000 in the same period. An initial seeding of 100,000 rat fibroblasts suspended in collagen increased to 163,000 cells in 2 days. An initial 100,000 human fibroblasts seeded in collagen decreased to 80,000 cells in 2 days. Retarded proliferation of human and gorilla fibroblasts in collagen is unrelated to a defect in DNA synthesis. By autoradiography human fibroblasts suspended in collagen incorporate labelled thymidine. By flow cytometry analysis, the DNA concentrations of human fibroblasts suspended in collagen exhibited 41% in a 4N chromosome state, compared to 14% in monolayer culture. Nuclei of gorilla fibroblasts from collagen displayed 42% in a 4N state, compared to 19% in monolayer culture. With nuclei of rat fibroblasts from collagen, 14% were in a 4N state, compared to 9% in monolayer culture. Primate fibroblasts show a three-fold increase in the number of nuclei in a 4N state compared to rat fibroblasts suspended in collagen. After replating fibroblasts released from collagen in monolayer culture in the presence of 1 mM hydroxyurea (an inhibitor of DNA synthesis) primate fibroblasts doubled in 24 hr. Under identical conditions, rat fibroblasts showed no cell division.(ABSTRACT TRUNCATED AT 250 WORDS)     

Identification of human specific gene duplications relative to other primates by array CGH and quantitative PCR

In order to identify human lineage specific (HLS) copy number differences (CNDs) compared to other primates, we performed pair wise comparisons (human vs. chimpanzee, gorilla and orangutan) by using cDNA array comparative genomic hybridization (CGH). A set of 23 genes with HLS duplications were identified, as well as other lineage differences in gene copy number specific of chimpanzee, gorilla and orangutan. Each species has gained more copies of specific genes rather than losing gene copies. Eleven of the 23 genes have only been observed to have undergone HLS duplication in Fortna et al. (2004) and in the present study. Then, seven of these 11 genes were analyzed by quantitative PCR in chimpanzee, gorilla and orangutan, as well as in other six primate species (Hylobates lar, Cercopithecus aethiops, Papio hamadryas, Macaca mulatta, Lagothrix lagothricha, and Saimiri sciureus). Six genes confirmed array CGH data, and four of them appeared to have bona fide HLS duplications (ABCB10, E2F6, CDH12, and TDG genes). We propose that these gene duplications have a potential to contribute to specific human phenotypes.     

Novel use of a chimpanzee pseudogene for chromosomal mapping of human cytochrome c oxidase subunit IV

We have isolated a chimpanzee processed pseudogene for subunit IV of cytochrome c oxidase (COX; EC 1.9.3.1) by screening a chimpanzee genomic library in lambda Charon 32 with a bovine liver cDNA encoding COX subunit IV (COX IV), and localized it to a 1.9-kb HindIII fragment. Southern-blot analysis of genomic DNA from five primates showed that DNAs from human, gorilla, and chimpanzee each contained the 1.9-kb pseudogene fragment, whereas orangutan and pigtail macaque monkey DNA did not. This result clearly indicates that the pseudogene arose before the divergence of the chimpanzee and gorilla from the primate lineage. By screening Chinese hamster x human hybrid panels with the human COX4 cDNA, we have mapped COX4 genes to two human chromosomes, 14 and 16. The 1.9-kb HindIII fragment containing the pseudogene, COX4P1, can be assigned to chromosome 14, and by means of rearranged chromosomes in somatic cell hybrids, to 14q21-qter. Similarly, the functional gene, COX4, has been mapped to 16q22-qter.     

Presence of influenza virus-reactive glycophorins other than glycophorin A in human erythrocyte membranes

The reactivities against seven hemagglutinins including influenza A and B viruses of six sialoglycoprotein (glycophorin) fractions, M-Frs.1-3 and N-Frs.1-3, separated from human OMs and ONs erythrocyte membranes by a combination of the LIS-phenol method and gel filtration were studied. The serological results show that M-Fr.1 and N-Fr.1 were glycophorins AM and AN, respectively, the reactivities against influenza A and B viruses of both M-Fr.2 and N-Fr.2 which contained glycophorins B and C were remarkably higher than that of glycophorin A and the reactivities against influenza viruses of both M-Fr.3 and N-Fr.3 which contained glycophorins B and D were considerably lower than that of glycophorin A.     

Evolution of glycophorin A in the hominoid primates studied with monoclonal antibodies, and description of a sialoglycoprotein analogous to human glycophorin B in chimpanzee

Comparison of human and primate erythrocyte membrane sialoglycoproteins showed that common chimpanzee, dwarf chimpanzee, gorilla, orangutan, and gibbon have major periodic acid Schiff-positive proteins resembling human glycophorin A (GPA) monomer and dimer in electrophoretic mobility on sodium dodecyl sulfate-polyacrylamide gels. Immunoperoxidase staining of Western blots with monoclonal antibodies to human GPA showed that these primate bands express some GPA antigenic determinants. A new sialoglycoprotein analogous to human glycophorin B (GPB) was detected in common chimpanzee. Although human MN blood group phenotype results from an amino acid polymorphism of GPA, Western blots showed that in chimpanzee sialoglycoprotein (GPAch) always expresses the M blood group, whereas chimpanzee sialoglycoprotein (GPBch) expresses either the N blood group or a null phenotype. This result explains the detection of M and MN, but not of N, blood group phenotypes in chimpanzee. GPBch has higher apparent m.w. than human GPB, is present in the erythrocyte membrane in greater quantity than human GPB, and contains trypsin cleavage site(s) and the 10F7 determinant (both found on human GPA but not GPB). Expression of human GPA antigenic determinants was consistent with the phylogeny of the hominoid primates; common and dwarf chimpanzee expressed most of the determinants tested, gorilla and orangutan an intermediate number, and gibbon and siamang the least. Of the GPA antigenic determinants examined, the MN blood group determinants were most consistently expressed during evolution of the hominoid primates. The results suggested that variability in expression of GPA antigenic determinants between species was due to both differences in amino acid sequence and glycosylation.     

Human genetic disorders, a phylogenetic perspective

When viewed from the perspective of time, human genetic disorders give new insights into their etiology and evolution. Here, we have correlated a specific set of Alu repetitive DNA elements, known to be the basis of certain genetic defects, with their phylogenetic roots in primate evolution. From a differential distribution of Alu repeats among primate species, we identify the phylogenetic roots of three human genetic diseases involving the LPL, ApoB, and HPRT genes. The different phylogenetic age of these genetic disorders could explain the different susceptibility of various primate species to genetic diseases. Our results show that LPL deficiency is the oldest and should affect humans, apes, and monkeys. ApoB deficiency should affect humans and great apes, while a disorder in the HPRT gene (leading to the Lesch-Nyhan syndrome) is unique to human, chimpanzee, and gorilla. Similar results can be obtained for cancer. We submit that de novo transpositions of Alu elements, and saltatory appearances of Alu-mediated genetic disorders, represent singularities, places where behavior changes suddenly. Alus' propensity to spread, not only increased the regulatory and developmental complexity of the primate genome, it also increased its instability and susceptibility to genetic defects and cancer. The dynamic spread not only provided markers of primate phylogeny, it must have actively shaped the course of that phylogeny.     

Evolutionary conservation of 5' upstream sequence of nine genes between human and great apes

Nucleotide sequences of nine 5' upstream gene regions for human, chimpanzee, gorilla, and orangutan were determined. We estimated nucleotide differences (d) for each region between human and great apes. The overall d was 0.027 (ranged from 0.004 to 0.052). Rates of nucleotide substitution were estimated by using d and divergence times of human, chimpanzee, gorilla, and orangutan. The overall rate of nucleotide substitution between human and other hominoids was estimated to be 0.52-0.85 x 10(-9). This rate in 5' upstream regions was lower than that of synonymous sites, suggesting that 5' upstream regions have evolved under some functional constraints. Because lower rates have been reported for coding sequences in primates compared to rodents, we also estimated the rate (1.17-1.76 x 10(-9)) of nucleotide substitutions for the corresponding 5' upstream regions in rodents (mouse/rat comparison). Thus the primate rate was lower than rodent rate also for the 5' upstream regions.     

Gorilla society: What we know and don't know

Science is fairly certain that the gorilla lineage separated from the remainder of the hominoid clade about eight million years ago, 2 , 4 and that the chimpanzee lineage and hominin clade did so about a million years after that. 1 , 2 However, just this year, 2007, it was discovered that although the human head louse separated from the congeneric chimpanzee body louse (Pediculus) around the same time as the chimpanzee and hominin lineages split, 3 the human pubic louse apparently split from its sister species, the congeneric gorilla louse, Pthirus, 4.5 million years after their host lineages split. 3 No tested explanations exist for the discrepancy. Much is known about hominin evolution, but much remains to be discovered. The same is true of primate socioecology in general and gorilla socioecology in particular.