Exon shuffling mimicked in cell culture

Expression of evolutionarily novel genes in tumors

The evolutionarily novel genes originated through different molecular mechanisms are expressed in tumors. Sometimes the expression of evolutionarily novel genes in tumors is highly specific. Moreover positive selection of many human tumor-related genes in primate lineage suggests their involvement in the origin of new functions beneficial to organisms. It is suggested to consider the expression of evolutionarily young or novel genes in tumors as a new biological phenomenon, a phenomenon of TSEEN (tumor specifically expressed, evolutionarily novel) genes.

alpha-Lipoic acid alters post-translational modifications and protects the chaperone activity of lens alpha-crystallin in naphthalene-induced cataract

PURPOSE

To evaluate whether alpha-lipoic acid (LA) inhibits lens opacity of naphthalene-induced cataract by altering post-translational modifications (PTMs) and protecting the chaperone activity of alpha-crystallins.

METHODS

Forty-five Sprague-Dawley rats were divided into three groups: control, naphthalene, and naphthalene plus LA. Cataracts were induced by oral administration of 1 g naphthalene/kg body weight/day. Rats in the naphthalene plus LA group were also fed 30 mg LA/day. The development of naphthalene-initiated cataract was monitored every week by slit lamp microscopy for nine weeks, then the lens proteins were separated by HPLC, and peaks corresponding to alpha-crystallins were resolved on 2-DE. The spots of 2-DE were subjected to mass spectrometry to identify PTMs. Chaperone activity of alpha-crystallins was measured by heat-induced aggregation of betaL-crystallin.

RESULTS

The lenses of rats fed with naphthalene plus LA exhibited less light scattering than that fed with only naphthalene at three weeks after treatment (P < 0.01). C-terminal truncated alphaA crystallin was detected in naphthalene-induced cataract and was abrogated by LA treatment. Several other post-translational modifications were identified including methylation, phosphorylation, acetylation, carbamylation, and oxidation.

CONCLUSIONS

Our data are the first to show PTM changes induced by naphthalene in rat lenses. Our findings also indicate that LA can inhibit naphthalene-induced lens opacity by altering PTM and protecting the chaperone activity of alpha-crystallins.

Evolution in health and medicine Sackler colloquium: Genomic disorders: a window into human gene and genome evolution

Gene duplications alter the genetic constitution of organisms and can be a driving force of molecular evolution in humans and the great apes. In this context, the study of genomic disorders has uncovered the essential role played by the genomic architecture, especially low copy repeats (LCRs) or segmental duplications (SDs). In fact, regardless of the mechanism, LCRs can mediate or stimulate rearrangements, inciting genomic instability and generating dynamic and unstable regions prone to rapid molecular evolution. In humans, copy-number variation (CNV) has been implicated in common traits such as neuropathy, hypertension, color blindness, infertility, and behavioral traits including autism and schizophrenia, as well as disease susceptibility to HIV, lupus nephritis, and psoriasis among many other clinical phenotypes. The same mechanisms implicated in the origin of genomic disorders may also play a role in the emergence of segmental duplications and the evolution of new genes by means of genomic and gene duplication and triplication, exon shuffling, exon accretion, and fusion/fission events.

The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans

We recently proposed a DNA replication-based mechanism of fork stalling and template switching (FoSTeS) to explain the complex genomic rearrangements associated with a dysmyelinating central nervous system disorder in humans. The FoSTeS mechanism has been further generalized and molecular mechanistic details have been provided in the microhomology-mediated break-induced replication (MMBIR) model that may underlie many structural variations in genomes from all domains of life. Here we provide evidence that human genomic rearrangements ranging in size from several megabases to a few hundred base pairs can be generated by FoSTeS/MMBIR. Furthermore, we show that FoSTeS/MMBIR-mediated rearrangements can occur mitotically and can result in duplication or triplication of individual genes or even rearrangements of single exons. The FoSTeS/MMBIR mechanism can explain both the gene duplication-divergence hypothesis and exon shuffling, suggesting an important role in both genome and single-gene evolution.

Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila

Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. Such examples are consistent with the classic model for exon shuffling, which relies on non-homologous recombination. However, recent data for chromosomal aberrations in model organisms suggest that ectopic homology-dependent recombination may also be important. Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements. Here we use ∼7,000 cDNA probes (∼112,000 primary images) to screen eight species within the Drosophila melanogaster subgroup and identify 17 duplicates that were generated through ectopic recombination within the last 12 mys. Most of these are functional and have evolved divergent expression patterns and novel chimeric structures. Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species.

In numerous organisms, many new genes have been found to originate through dispersed gene duplication and exon/domain shuffling. What recombination mechanisms were involved in the duplication and the shuffling processes? Lack of the intermediate products of recombination that share adequate sequence identity between homologous sequences, or the parental sequences from which the new genes were derived, often makes answering these questions difficult. We identified a number of young genes that originated in recently diverged branches in the evolutionary tree of the eight Drosophila melanogaster subgroup species, by using fluorescence in situ hybridization with polytene chromosomes. We analyzed the genomic regions surrounding 17 new dispersed duplicate genes and observed that most of these genes are flanked by repetitive elements (REs), including a large and diverged transposable element family, DNAREP1. Several copies of these REs are kept in both new and parental gene regions, and their degeneration is correlated with the increasing ages of the identified new genes. These data suggest that REs mediate the recombination responsible for the new gene origination.

Transposition of reversed Ac element ends generates novel chimeric genes in maize

The maize Activator/Dissociation (Ac/Ds) elements are members of the hAT (hobo, Ac, and Tam3) superfamily of type II (DNA) transposons that transpose through a "cut-and-paste" mechanism. Previously, we reported that a pair of Ac ends in reversed orientation is capable of undergoing alternative transposition reactions that can generate large-scale chromosomal rearrangements, including deletions and inversions. We show here that rearrangements induced by reversed Ac ends transposition can join the coding and regulatory sequences of two linked paralogous genes to generate a series of chimeric genes, some of which are functional. To our knowledge, this is the first report demonstrating that alternative transposition reactions can recombine gene segments, leading to the creation of new genes.

Promoter shuffling at a nuclear gene for mitochondrial RPL27. Involvement of interchromosome and subsequent intrachromosome recombinations

The Reclinomonas americana mitochondrial genome contains a mitochondrial ribosomal protein L27 (rpl27) gene, whereas the rpl27 gene is absent from all plant mitochondrial genomes examined to date. This suggests that plant mitochondrial rpl27 genes have been transferred previously from the mitochondrial genome to the nuclear genome. A nuclear cDNA encoding mitochondrial RPL27 was identified in rice (Oryza sativa). Three similar sequences were identified: rpl27-1 and rpl27-2 on chromosome 8 and rpl27-3 on chromosome 4. Harr plot analysis suggests that they were generated by inter- and intrachromosomal duplications. Interestingly, the transcribed rpl27 gene (rpl27-1) acquired a promoter sequence that was derived from the rice spt16 (Osspt16) gene, the homolog of a global transcription factor in yeast (Saccharomyces cerevisiae) located downstream from the rpl27-3 sequence on chromosome 4, after inter- and intrachromosomal recombination. Reverse transcription-PCR and promoter assay revealed that the rpl27 mRNAs were mainly transcribed from rpl27-1. A repeat of seven nucleotides (AATAGTT) was identified at the junction of rpl27-1 and rpl27-2 on chromosome 8, and the same repeat was also identified at the 5' end of rpl27-2 and the 3' end of rpl27-1. This repeat (AATAGTT) contains the hot-spot sequence AGTT, which is preferentially recognized by topoisomerase I in wheat (Triticum aestivum) germ, suggesting the involvement of topoisomerase I in this recombination. We here report the example of promoter shuffling and show that this promoter shuffling resulted from a recent segmental duplication through inter- and intrachromosomal recombination events.

Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila

The formation of chimeric gene structures provides important routes by which novel proteins and functions are introduced into genomes. Signatures of these events have been identified in organisms from wide phylogenic distributions. However, the ability to characterize the early phases of these evolutionary processes has been difficult due to the ancient age of the genes or to the limitations of strictly computational approaches. While examples involving retrotransposition exist, our understanding of chimeric genes originating via illegitimate recombination is limited to speculations based on ancient genes or transfection experiments. Here we report a case of a young chimeric gene that has originated by illegitimate recombination in Drosophila. This gene was created within the last 2–3 million years, prior to the speciation of Drosophila simulans, Drosophila sechellia, and Drosophila mauritiana. The duplication, which involved the Bällchen gene on Chromosome 3R, was partial, removing substantial 3′ coding sequence. Subsequent to the duplication onto the X chromosome, intergenic sequence was recruited into the protein-coding region creating a chimeric peptide with ~ 33 new amino acid residues. In addition, a novel intron-containing 5′ UTR and novel 3′ UTR evolved. We further found that this new X-linked gene has evolved testes-specific expression. Following speciation of the D. simulans complex, this novel gene evolved lineage-specifically with evidence for positive selection acting along the D. simulans branch.

Illegitimate recombination, the non-homologous recombination that occurs between DNA sequences with few or no identical nucleotides, is a general phenomenon that has been known to cause many medically important deleterious changes. However, little is known about the positive side of such a process. For example, little is known about its relative role in the origin of new gene functions that confer increased fitness to species. This work contributes to the understanding of the significance of this process. Here the authors report on a young chimeric gene that has originated by illegitimate recombination in Drosophila. The term “chimeric gene” refers to gene structures—both coding and noncoding—which have been generated from distinct parental loci. This chimeric gene was created within the last 2–3 million years, prior to the speciation of Drosophila simulans, Drosophila sechellia, and Drosophila mauritiana. A gene on Chromosome 3R was duplicated onto the X chromosome and recruited intergenic sequence, creating a chimeric peptide. It was found that this new X-linked gene has evolved testes-specific expression. Following speciation of the D. simulans complex, this novel gene evolved lineage-specifically under positive Darwinian selection.

B1 and related SINEs in mammalian genomes

Although B1 and Alu were the first discovered Short Interspersed Elements (SINEs), the studies of these genomic repeats were mostly limited to mice and humans and little data on their presence in other animals were available. Here we report the presence of these SINEs in a wide range of rodents (in all 15 tested families) as well as primates and tree-shrews and their absence in other mammals. Distribution pattern of these SINEs in mammals supports close relationship between rodents and primates as well as tree-shrews. Sequence analysis of these elements, apparently descending from cellular 7SL RNA indicates their rearrangements such as dimerization (Alu), quasi-dimerization (B1), acquiring a tRNA-related unit (B1-dID), extended deletions, etc., preceding their active expansion in the genomes. The revealed common pattern of microenvironment of some rearrangement hot spots in SINEs (internal duplications and deletions) suggests involvement of short direct repeats in the mechanism of such rearrangements. This hypothesis allows us to explain short rearrangements in these and other short retroposons.

The origin of new genes: glimpses from the young and old

Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.

Evolution of novel genes

Much progress in understanding the evolution of new genes has been accomplished in the past few years. Molecular mechanisms such as illegitimate recombination and LINE element mediated 3' transduction underlying exon shuffling, a major process for generating new genes, are better understood. The identification of young genes in invertebrates and vertebrates has revealed a significant role of adaptive evolution acting on initially rudimentary gene structures created as if by evolutionary tinkers. New genes in humans and our primate relatives add a new component to the understanding of genetic divergence between humans and non-humans.

Characteristics of super alphaA-crystallin, a product of in vitro exon shuffling

alphaA-Crystallin, a small heat shock protein with chaperone-like activity, forms dynamic multimeric complexes. Recently we described the spontaneous generation of a mutant protein (super alphaA-crystallin) by exon duplication arisen via exon shuffling confirming a classic hypothesis by Gilbert [Nature 271 (1978) 501]. Comparison of super alphaA-crystallin, which is viable in a mouse skeletal muscle cell line, with normal alphaA-crystallin shows that it has diminished thermostability, increased exposure of hydrophobic patches, a larger complex size and lost its chaperone activity. However, super alphaA-crystallin subunits exchange as readily between complexes as does normal alphaA-crystallin. These data indicate that chaperone-like activity may vanish independent of subunit hydrophobicity and exchangeability.

Demyelination and axonal dystrophy in alpha A-crystallin transgenic mice

Homozygous mice transgenic for alphaA-crystallin, one of the structural eye lens proteins, developed hindlimb paralysis after 8 weeks of age. To unravel the pathogenesis of this unexpected finding and the possible role of alphaA-crystallin in this pathological process, mice were subjected to a histopathological and immunohistochemical investigation. Immunohistochemistry showed large deposits of alphaA-crystallin in the astrocytes of the spinal cord, and in the Schwann cells of dorsal roots and sciatic nerves. Additionally, microscopy showed dystrophic axons in the spinal cord and digestion chambers as a sign of ongoing demyelination in dorsal roots and sciatic nerves. Apart from a few areas with slight alphaA-crystallin-immunopositive structures, the brain was normal. Because the alphaA-crystallin protein expression appeared in specific cells of the nervous system (astrocytes and Schwann cells), the most plausible explanation for the paralysis is a disturbance of cell function caused by the excessive intracytoplasmic accumulation of the alphaA-crystallin protein. This is followed by a sequence of secondary changes (demyelination, axonal dystrophy) and finally arthrosis. In conclusion, alphaA-crystallin transgenic mice develop a peripheral and central neuropathy primarily affecting spinal cord areas at the dorsal side, dorsal root and sciatic nerve.