Introns increase gene expression in cultured maize cells

Using electroporation-mediated gene transfer, the gene encoding the Slow (S) migrating polypeptide of the maize (Zea mays L.) alcohol dehydrogenase-1 (Adh1) enzyme has been introduced stably and transiently into maize cells containing an endogenous Fast (F) ADH1 electromorph. In stable transformants an 11.5-kb fragment was sufficient to program normal S expression relative to the endogenous F allele. In transient assays, Adh1-S gene constructs lacking the 9 Adh1-S intervening sequences (introns) were expressed at levels 50- to 100-fold less than the intact gene; the presence of intron 1 alone restored levels of gene expression to those found with the intact gene. The last two introns also stimulate Adh1-S expression, but the level is threefold below that of the intact gene. The expression of a chimeric chloramphenicol acetyltransferase (CAT) gene utilizing the 5' promoter and 3' polyadenylation regions of the Adh1 gene was increased 100-fold by the addition of sequences containing the Adh1 intron 1. The Adh1 intron 1 sequences did not stimulate CAT expression when located outside the transcribed region. When located within the transcribed region, the Adh1 intron 1 region efficiently stimulated CAT expression only when located between the promoter and the CAT coding region. A construct containing the Adh1 intron 1 fragment produced 40-fold more mRNA than a construct containing an equivalent cDNA fragment. Both the Adh1 intron 1 and the intron from a second maize gene, Bronze1, stimulated expression from other promoters (cauliflower mosaic virus 35S and nopaline synthase) and of other coding regions (luciferase and neomycin phosphotransferase II) as well. These results indicated that introns increase both Adh1 and chimeric gene expression in maize and the optimal location for such an intron is near the 5' end of the mRNA.     

Structure and evolution of mouse interleukin 6 gene

Restriction fragment length polymorphism in the interleukin 6 gene of murine rodents extending phylogenetically from Mus musculus domesticus to the rat has been analyzed. Most species exhibit distinct restriction site patterns. In contrast, limited polymorphism was found in the tumor necrosis factor alpha gene indicating different selective pressure acting on both genes. The gene encoding interleukin 6 was isolated from a genomic library and the exon/intron organization was determined by restriction analysis and limited DNA sequence analysis. It consists of five exons which distribute over about seven kilobases, thus resembling in structure and organization the human counterpart. Furthermore, no restriction fragment length polymorphisms in the interleukin 6 gene of autoimmune strains NZB, NZW, MRL-lpr/lpr and BxSB could be detected for either EcoRI, BamHI or HindIII.     

Structure and evolution of the largest chloroplast gene (ORF2280): internal plasticity and multiple gene loss during angiosperm evolution

We have determined the nucleotide sequence of the Pelargonium x hortorum ORF2280 homolog, the largest gene in the plastid genome of most land plants, and compared it to published homologs from Nicotiana tabacum, Epifagus virginiana, Spinacia oleracea, and Marchantia polymorpha. Multiple alignment of protein sequences requires an extraordinary number of gaps, indicating a very high frequency of insertion/deletion events during the evolution of the protein; however, the overall predicted size of the protein varies relatively little among the five species. At 2 109 codons, the Pelargonium gene is smaller than other land plant ORF2280 homologs and exhibits a rate of nucleotide substitution several times higher relative to Nicotiana, Epifagus, and Spinacia. Southern-blot and restriction-mapping studies were carried out to uncover length variation in ORF2280 homologs from 279 species (representing 111 families) of angiosperms. In many independent angiosperm lineages, this gene has sustained deletions ranging in size from 200 bp to almost 6 kb. Based on the severity of deletions, we postulate that the chloroplast homolog of ORF2280 has become nonfunctional in at least four independent lineages of angiosperms.     

Gene conversion and the evolution of protocadherin gene cluster diversity

The synaptic cell adhesion molecules encoded by the protocadherin gene cluster are hypothesized to provide a molecular code involved in the generation of synaptic complexity in the developing brain. Variation in copy number and sequence content of protocadherin cluster genes among vertebrate species could reflect adaptive differences in protocadherin function. We have completed an analysis of zebrafish protocadherin cluster genes. Zebrafish have two unlinked protocadherin clusters, DrPcdh1 and DrPcdh2. Like mammalian protocadherin clusters, DrPcdh1 has both α and γ variable and constant region exons. A consensus protocadherin promoter motif sequence identified in mammals is also conserved in zebrafish. Few orthologous relationships, however, are apparent between zebrafish and mammalian protocadherin proteins. Here we show that protocadherin cluster genes in human, mouse, rat, and zebrafish are subject to striking gene conversion events. These events are restricted to regions of the coding sequence, particularly the coding sequences of ectodomain 6 and the cytoplasmic domain. Diversity among paralogs is restricted to particular ectodomains that are excluded from conversion events. Conversion events are also strongly correlated with an increase in third-position GC content. We propose that the combination of lineage-specific duplication, restricted gene conversion, and adaptive variation in diversified ectodomains drives vertebrate protocadherin cluster evolution.     

Characterization of the laminin gene family and evolution in zebrafish

Laminins are essential components of all basement membranes and are fundamental to tissue development and homeostasis. Humans possess at least 16 different heterotrimeric laminin complexes formed through different combinations of alpha, beta, and gamma chains. Individual chains appear to exhibit unique expression patterns, leading to the notion that overlap between expression domains governs the constitution of complexes found within particular tissues. However, the spatial and temporal expression of laminin genes has not been comprehensively analyzed in any vertebrate model to date. Here, we describe the tissue‐specific expression patterns of all laminin genes in the zebrafish, throughout embryonic development and into the “post‐juvenile” period, which is representative of the adult body form. In addition, we present phylogenetic and microsynteny analyses, which demonstrate that the majority of our zebrafish sequences are orthologous to human laminin genes. Together, these data represent a fundamental resource for the study of vertebrate laminins. Developmental Dynamics 240:422–431, 2011. © 2011 Wiley‐Liss, Inc.     

Structure and evolution of gene regulatory networks in microbial genomes

With the availability of genome sequences for hundreds of microbial genomes, it has become possible to address several questions from a comparative perspective to understand the structure and function of regulatory systems, at least in model organisms. Recent studies have focused on topological properties and the evolution of regulatory networks and their components. Our understanding of natural networks is paving the way to embedding synthetic regulatory systems into organisms, allowing us to expand the natural diversity of living systems to an extent we had never before anticipated.     

The plasticity of immunoglobulin gene systems in evolution

Summary: The mechanism of recombination‐activating gene (RAG)‐mediated rearrangement exists in all jawed vertebrates, but the organization and structure of immunoglobulin (Ig) genes, as they differ in fish and among fish species, reveal their capability for rapid evolution. In systems where there can exist 100 Ig loci, exon restructuring and sequence changes of the constant regions led to divergence of effector functions. Recombination among these loci created hybrid genes, the strangest of which encode variable (V) regions that function as part of secreted molecules and, as the result of an ancient translocation, are also grafted onto the T‐cell receptor. Genomic changes in V‐gene structure, created by RAG recombinase acting on germline recombination signal sequences, led variously to the generation of fixed receptor specificities, pseudogene templates for gene conversion, and ultimately to Ig sequences that evolved away from Ig function. The presence of so many Ig loci in fishes raises interesting questions not only as to how their regulation is achieved but also how successive whole‐locus duplications are accommodated by a system whose function in other vertebrates is based on clonal antigen receptor expression.     

Adaptive evolution of young gene duplicates in mammals

Duplicate genes act as a source of genetic material from which new functions arise. They exist in large numbers in every sequenced eukaryotic genome and may be responsible for many differences in phenotypes between species. However, recent work searching for the targets of positive selection in humans has largely ignored duplicated genes due to complications in orthology assignment. Here we find that a high proportion of young gene duplicates in the human, macaque, mouse, and rat genomes have experienced adaptive natural selection. Approximately 10% of all lineage-specific duplicates show evidence for positive selection on their protein sequences, larger than any reported amount of selection among single-copy genes in these lineages using similar methods. We also find that newly duplicated genes that have been transposed to new chromosomal locations are significantly more likely to have undergone positive selection than the ancestral copy. Human-specific duplicates evolving under adaptive natural selection include a surprising number of genes involved in neuronal and cognitive functions. Our results imply that genome scans for selection that ignore duplicated loci are missing a large fraction of all adaptive substitutions. The results are also in agreement with the classical model of evolution by gene duplication, supporting a common role for neofunctionalization in the long-term maintenance of gene duplicates.Recently duplicated loci suffer one of two long-term fates: maintenance or loss (Ohno 1970; Walsh 1995). While pseudogenization is the more likely fate of recently duplicated genes, many models have been proposed that could lead to the long-term maintenance of multiple paralogs (Spofford 1969; Ohno 1970; Dykhuizen and Hartl 1980; Hughes 1994; Force et al. 1999; Stoltzfus 1999). The maintenance of duplicates can be a by-product of neutral evolution (Dykhuizen and Hartl 1980; Force et al. 1999; Stoltzfus 1999), or there can be adaptive substitutions either during (Spofford 1969; Ohno 1970) or after (Ohno 1970; Hughes 1994) the fixation of the duplicated locus. Previous studies have found signatures of adaptive evolution among individual duplicated genes, suggesting that selection for new functions (“neofunctionalization”) is the mechanism acting to retain new paralogs (Zhang et al. 1998; Merritt and Quattro 2001; Betran and Long 2003; Moore and Purugganan 2003; Rodriguez-Trelles et al. 2003; Thornton and Long 2005). While these studies support the neofunctionalization model, the genome-wide proportion of all duplicates fixed and maintained by natural selection is still not known (Hahn 2009).Gene duplication supplies the raw material necessary to evolve novel functions and is therefore a source of adaptive change. Previous studies in mammals have searched for positively selected genes in the hope of identifying the nucleotide substitutions that underlie phenotypic divergence between species, but these genome-wide scans have intentionally ignored duplicated loci in order to avoid problems in the assignment of orthology (Clark et al. 2003; Nielsen et al. 2005; Bakewell et al. 2007; Kosiol et al. 2008). This oversight is unfortunate, as many cases of adaptive evolution of individual gene duplicates are known (see above). These previous results from studies of individual gene families imply that by neglecting duplicated loci we are missing a substantial fraction of the adaptive events that differentiate species. Ignoring patterns of selection on duplicated loci in humans may be particularly shortsighted, as the rate of gene duplication has increased in our recent past (She et al. 2006; Hahn et al. 2007).Here we study the evolutionary forces acting on recent gene duplications in four mammalian genomes: human, macaque, rat, and mouse. By focusing on young duplicates we hope to capture the mechanisms responsible for the initial maintenance of new genes. We use codon-based likelihood models implemented in the PAML package (Yang 2007) to test for adaptive evolution shortly after the duplication. To ensure the accuracy of our results we also use non-likelihood-based methods and conduct a number of checks on our results. We find that a larger fraction of young duplicates have experienced positive selection than have a comparable set of single-copy orthologs. We also observe that, among duplicates, new paralogs that have moved to a different genomic location are more likely to experience adaptive evolution than are the copies in the original location.     

The role of sperm-mediated gene transfer in genome mutation and evolution

Contradictory evidence surrounds the claim that sperm cells are able to introduce exogenous DNA into the oocyte at the time of fertilisation. Although strong natural barriers exist against sperm-mediated gene transfer, such barriers are unlikely to be absolutely inviolable. If sperm cells can act as vectors for exogenous DNA, it follows that the genome of sexually reproducing animals may be subject to alteration by exogenous DNA sequences carried by sperm cells. At present there are insufficient data to permit quantification of the rate of sperm-mediated gene transfer. The implications of sperm-mediated gene transfer are significant and include evolutionary effects on the mammalian genome and pathologies in humans from de novo mutations. Despite the absence of firm data, geneticists would be wise to be vigilant to the potential consequences of sperm-mediated gene transfer.     

The master control gene for morphogenesis and evolution of the eye

The human Aniridia, the murine Small eye, and the eyeless mutations of Drosophila affect homologous (Pax-6) genes that contain both a paired- and a homeobox. By ectopic expression of these genes, functional eyes can be induced on the legs, wings, and antennae of the fly, indicating that eyeless (Pax-6) is the master control gene for eye morphogenesis. The finding of Pax-6 from flatworms to humans suggests that eyeless is a universal master control gene and that the various types of eyes in the various animal phyla may have evolved from a single prototype.     

SNPs in disease gene mapping, medicinal drug development and evolution

Single nucleotide polymorphism (SNP) technologies can be used to identify disease-causing genes in humans and to understand the inter-individual variation in drug response. These areas of research have major medical benefits. By establishing an association between the genetic make-up of an individual and drug response it may be possible to develop a genome-based diet and medicines that are more effective and safer for each individual. Additionally, SNPs can be used to understand the molecular mechanisms of sequence evolution. It has been found that throughout the given gene, the rate, type and site of nucleotide substitutions as well as the selection pressure on codons is not uniform. The residues that evolve under strong selective pressures are found to be significantly associated with human disease. Deleterious mutations that affect biological function of proteins are effectively being rejected by natural selection from the gene pool. If substituted nucleotides are fixed during evolution then they may have selection advantages, they may be neutral, or they may be deleterious and cause pathology. Therefore, it is possible that disease-associated SNPs (or pathology) and evolution can be related to one another.     

Phylogenetically Older Introns Strongly Correlate With Module Boundaries in Ancient Proteins

The hypothesis that some (but not all) introns were used to construct ancient genes by exon shuffling of modules at the earliest stages of evolution is supported by the finding of an excess of phase-zero intron positions in the boundary regions of such modules in 276 ancient proteins (defined as common to eukaryotes and prokaryotes). Here we show further that as phase-zero intron positions are shared by distant taxa, and thus are truly phylogenetically ancient, their excess in the boundaries becomes greater, rising to an 80% excess if shared by four out of the five taxa: vertebrates, invertebrates, fungi, plants, and protists.     

The origin and evolution of human ampliconic gene families and ampliconic structure

Out of the nine male-specific gene families in the human Y chromosome amplicons, we investigate the origin and evolution of seven families for which gametologous and orthologous sequences are available. Proto-X/Y gene pairs in the original mammalian sex chromosomes played major roles in origins and gave rise to five gene families: XKRY, VCY, HSFY, RBMY, and TSPY. The divergence times between gametologous X- and Y-linked copies in these families are well correlated with the former X-chromosomal locations. The CDY and DAZ families originated exceptionally by retroposition and transposition of autosomal copies, respectively, but CDY possesses an X-linked copy of enigmatic origin. We also investigate the evolutionary relatedness among Y-linked copies of a gene family in light of their ampliconic locations (palindromes, inverted repeats, and the TSPY array). Although any pair of copies located at the same arm positions within a palindrome is identical or nearly so by frequent gene conversion, copies located at different arm positions are distinctively different. Since these and other distinct copies in various gene families were amplified almost simultaneously in the stem lineage of Catarrhini, we take these simultaneous amplifications as evidence for the elaborate formation of Y ampliconic structure. Curiously, some copies in a gene family located at different palindromes exhibit high sequence similarity, and in most cases, such similarity greatly extends to repeat units that harbor these copies. It appears that such palindromic repeat units have evolved by and large en bloc, but they have undergone frequent exchanges between palindromes.     

A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast

It is widely accepted that newly arisen duplicate gene pairs experience an altered selective regime that is often manifested as an increase in the rate of protein sequence evolution. Many details about the nature of the rate acceleration remain unknown, however, including its typical magnitude and duration, and whether it applies to both gene copies or just one. We provide initial answers to these questions by comparing the rate of protein sequence evolution among eight yeast species, between a large set of duplicate gene pairs that were created by a whole-genome duplication (WGD) and a set of genes that were returned to single-copy after this event. Importantly, we use a new method that takes into account the tendency for slowly evolving genes to be retained preferentially in duplicate. We show that, on average, proteins encoded by duplicate gene pairs evolved at least three times faster immediately after the WGD than single-copy genes to which they behave identically in non-WGD lineages. Although the high rate in duplicated genes subsequently declined rapidly, it has not yet returned to the typical rate for single-copy genes. In addition, we show that although duplicate gene pairs often have highly asymmetric rates of evolution, even the slower members of pairs show evidence of a burst of protein sequence evolution immediately after duplication. We discuss the contribution of neofunctionalization to duplicate gene preservation and propose that a form of subfunctionalization mediated by coding region activity-reducing mutations is likely to have played an important role.     

DAZ gene copies: evidence of Y chromosome evolution

The DAZ gene, a contributing factor in infertility, lies on the human Y chromosome's AZFc region, whose deletion is a common cause of spermatogenic failure. Y chromosome binary polymorphisms on the non-recombining Y (NRY) region, believed to be a single occurrence on an evolutionary scale, were typed in a sample of fertile and infertile men with known DAZ backgrounds. The Y single-nucleotide polymorphisms (Y-SNPs) with low mutation rates are currently well characterized and permit the construction of a unique phylogeny of haplogroups. DAZ haplotypes were defined using single-nucleotide variant (SNV)/sequence tagged-site (STS) markers to distinguish between the four copies of the gene. The variation of 10 Y chromosome short tandem repeat (STRs) was used to determine the coalescence age of DAZ haplotypes in a comparable time frame similar to that of SNP haplogroups. An association between DAZ haplotypes and Y chromosome haplogroups was found, and our data show that the DAZ gene is not under selective constraints and its evolution depends only on the mutation rate. The same variants were common to fertile and infertile men, although partial DAZ deletions occurred only in infertile men, suggesting that those should only be used as a tool for infertility diagnosis when analysed in combination with haplogroup determinations.