The evolution of a plant globin gene family

Summary We have analyzed the sequences of soybean leghemoglobin genes as an initial step toward understanding their mode of evolution. Alignment of the sequences of plant globin genes with those of animals reveals that (i) based on the proportion of nucleotide substitutions that have occurred at the first, second, and third codon positions, the time of divergence of plant and animal globin gene families appears to be extremely remote (between 900 million and 1.4 billion years ago, if one assumes constancy of evolutionary rate in both the plant and animal lineages) and (ii) in addition to the normal regulatory sequences on the 5 end, an approximately 30-base-pair sequence, specific to globin genes, that surrounds the cap site is conserved between the plant and animal globin genes. Comparison of the leghemoglobin sequences with one another shows that (i) the relative amount of sequence divergence in various coding and noncoding regions is roughly similar to that found for animal globin genes and (ii) as in animal globin genes, the positions of insertions and deletions in the intervening sequences often coincide with the locations of direct repeats. Thus, the mode of evolution of the plant globin genes appears to resemble, in many ways, that of their animal counterparts. We contrast the overall intergenic organization of the plant globin genes with that of animal genes, and discuss the possibility of the concerted evolution of the leghemoglobin genes.     

Evolution of the rat kallikrein gene family: Gene conversion leads to functional diversity

Summary Kallikrein-like simple serine proteases are encoded by closely related members of a gene family in several mammalian species. Molecular cloning and genomic Southern blot analysis after conventional and pulsed-field gel electrophoresis indicate that the rat kallikrein gene family comprises 15–20 members, probably closely linked at a single locus. Determination of the nucleotide sequences of the rGK-3,-4, and-6 genes here completes sequence data for a total of nine rat kallikrein family members. Comparison of the rat gene sequences to each other and to those of human and mouse kallikrein family genes reveals patterns of relatedness indicative of concerted evolution. Analysis of nucleotide sequence variants in kallikrein family members shows that most sequence variants are shared by multiple family members; the patterns of shared variants are complex and indicate multiple short gene conversions between family members. Sequence exchanges between family members generate novel assortments of variants in amino acid coding regions that may affect substrate specificity and thereby contribute to the diversity of enzyme activity. Furthermore, small sequence exchanges also may play a role in generating the diverse patterns of tissue-specific expression of rat family members. These analyses indicate an important role for gene conversion in the evolution of the functional diversity of these duplicated genes.     

Characterization of the cow stomach lysozyme genes: Repetitive DNA and concerted evolution

Cow stomach lysozyme genes have evolved in a mosaic pattern. The majority of the intronic and flanking sequences show an amount of sequence difference consistent with divergent evolution since duplication of the genes 40–50 million years ago. In contrast, exons 1, 2, and 4 and immediately adjacent intronic sequences differ little between genes and show evidence of recent concerted evolution. Exon 3 appears to be evolving divergently. The three characterized genes vary from 5.6 to 7.9 kilobases in length. Different distributions of repetitive DNA are found in each gene, which accounts for the majority of length differences between genes. The different distributions of repetitive DNA in each gene suggest the repetitive elements were inserted into each gene after the duplications that give rise to these three genes and provide additional support for divergent evolution for the majority of each gene. The observation that intronic and flanking sequences are evolving divergently suggests that the concerted evolution events involved in homogenizing the coding regions of lysozyme genes involve only one exon at a time. This model of concerted evolution would allow the shuffling of exon-sized pieces of information between genes, a phenomenon that may have aided in the early adaptive evolution of stomach lysozyme.Deceased July 21, 1991 Correspondence to: D.M. Irwin     

Adaptive evolution in the rat olfactory receptor gene family

Summary Comparison of DNA sequences of the rat (Rattus norvegicus) olfactory receptor gene family revealed an unusual pattern of nucleotide substitution in the gene region encoding the second extracellular domain (E2) of the protein. In this domain, nonsynonymous nucleotide differences between members of this subfamily that caused a change in amino acid residue polarity were over four times more frequent than nonsynonymous differences that did not cause a polarity change. This nonrandom pattern of nucleotide substitution is evidence of past directional selection favoring diversification of the E2 domain among members of this subfamily. This in turn suggests that E2 may play some important role in the functions unique to each member of the olfactory receptor family, and that it may perhaps be an odorant binding domain.Offprint requests to: A.L. Hughes     

A novel fatty acid-binding protein (FABP) gene resulting from tandem gene duplication in mammals: transcription in rat retina and testis

We have identified a new member of the FABP gene family, designated FABP12. FABP12 has the same structure as other FABP genes and resides in a cluster with FABP4/5/8/9 within 300,000 bp chromosomal region. FABP12 orthologs are found in mammals, but not in the zebrafish or chicken genomes. We demonstrate that FABP12 is expressed in rodent retina and testis, as well as in human retinoblastoma cell lines. In situ hybridization of adult rat retinal tissue indicates that FABP12 mRNA is expressed in ganglion and inner nuclear layer cells. Analysis of adult rat testis reveals a pattern of expression that is different from that of the known testis FABP (FABP9) in the testicular germ cells, suggesting distinct roles for these two genes during mammalian spermatogenesis. We propose that FABP12 arose as the result of tandem gene duplication, a mechanism that may have been instrumental to the expansion of the FABP family.     

Evolution of a multigene family that encodes the Kunitz chymotrypsin inhibitor in winged bean: a possible intermediate in the generation of a new gene with a distinct pattern of expression

Winged bean Kunitz chymotrypsin inhibitor (WCI) accumulates in an organ-specific and temporally regulated manner. The protein is encoded by a multigene family that includes at least four putative inhibitor-coding genes and three pseudogenes. The structure of the WCI genes indicates that an insertion at a 5′ proximal site occurred after duplication of the ancestral WCI gene and that several gene conversion events subsequently contributed to the evolution of this gene family. Analysis of the promoter activity of the 5′ regions of the WCI genes in transgenic tobacco showed that only the 5′ regions of the WCI-3a and WCI-3b genes, which encode the major WCI protein in winged bean, promoted the organ-specific and temporally regulated expression of a reporter gene. The 5′ region of a pseudogene, the WCI-P1 gene which contains frameshift mutations, exhibited constitutive promoter activity in tobacco, an indication that the 5′ region of the WCI-P1 gene might spontaneously have acquired new regulatory sequences during evolution. Since gene conversion is a relatively frequent event and since the homology between the WCI-P1 and WCI-3a/b genes is disrupted at a 5′ proximal site by remnants of an inserted sequence, the WCI-P1 gene appears to be a possible intermediate that could be converted into a new functional gene with a distinct pattern of expression by a single gene-conversion event. Received: 17 April 1996 / Accepted: 23 October 1996     

Molecular evolution of the vertebrate hexokinase gene family: Identification of a conserved fifth vertebrate hexokinase gene

Hexokinases (HK) phosphorylate sugar immediately upon its entry into cells allowing these sugars to be metabolized. A total of four hexokinases have been characterized in a diversity of vertebrates—HKI, HKII, HKIII, and HKIV. HKIV is often called glucokinase (GCK) and has half the molecular weight of the other hexokinases, as it only has one hexokinase domain, while other vertebrate HKs have two. Differing hypothesis has been proposed to explain the diversification of the hexokinase gene family. We used a genomic approach to characterize hexokinase genes in a diverse array of vertebrate species and close relatives. Surprisingly we identified a fifth hexokinase-like gene, HKDC1 that exists and is expressed in diverse vertebrates. Analysis of the amino acid sequence of HKDC1 suggests that it may function as a hexokinase. To understand the evolution of the vertebrate hexokinase gene family we established a phylogeny of the hexokinase domain in all of the vertebrate hexokinase genes, as well as hexokinase genes from close relatives of the vertebrates. Our phylogeny demonstrates that duplication of the hexokinase domain, yielding a HK with two hexokinase domains, occurred prior to the diversification of the hexokinase gene family. We also establish that GCK evolved from a two hexokinase domain-containing gene, but has lost its N-terminal hexokinase domain. We also show that parallel changes in enzymatic function of HKI and HKIII have occurred.     

The genomic organization and evolution of the natural killer immunoglobulin-like receptor (KIR) gene cluster

Natural killer (NK) immunoglobulin-like receptors (KIRs) are a family of polymorphic receptors which interact with specific motifs on HLA class I molecules and modulate NK cytolytic activity. In this study, we analyzed a recently sequenced subgenomic region on chromosome 19q13.4 containing eight members of the KIR receptor repertoire. Six members are clustered within a 100-kb continuous sequence. These genes include a previously unpublished member of the KIR gene family 2DS6, as well as 2DL1, 2DL4, 3DL1, 2DS4, 3DL2, from centromere to telomere. Two additional KIR genes, KIRCI and 2DL3, which may be located centromeric of this cluster were also analyzed. We show that the KIR genes have undergone repeated gene duplications. Diversification between the genes has occurred postduplication primarily as a result of retroelement indels and gene truncation. Using pre- and postduplication Alu sequences identified within these genes as evolutionary molecular clocks, the evolution and duplication of this gene cluster is estimated to have occurred 30–45 million years ago, during primate evolution. A proposed model of the duplication history of the KIR gene family leading to their present organization is presented. Received: 25 November 1999 / Revised: 10 January 2000     

Increased rate of hair keratin gene loss in the cetacean lineage

Background

Hair represents an evolutionary innovation that appeared early on mammalian evolutionary history, and presumably contributed significantly to the rapid radiation of the group. An interesting event in hair evolution has been its secondary loss in some mammalian groups, such as cetaceans, whose hairless phenotype appears to be an adaptive response to better meet the environmental conditions. To determine whether different repertoire of keratin genes among mammals can potentially explain the phenotypic hair features of different lineages, we characterized the type I and II clusters of alpha keratins from eight mammalian species, including the hairless dolphin and minke whale representing the order Cetacea.

Results

We combined the available genomic information with phylogenetic analysis to conduct a comprehensive analysis of the evolutionary patterns of keratin gene clusters. We found that both type I and II gene clusters are fairly conserved among the terrestrial mammals included in this study, with lineage specific gene duplication and gene loss. Nevertheless, there is also evidence for an increased rate of pseudogenization in the cetacean lineage when compared to their terrestrial relatives, especially among the hair type keratins.

Conclusions

Here we present a comprehensive characterization of alpha-keratin genes among mammals and elucidate the mechanisms involved in the evolution of this gene family. We identified lineage-specific gene duplications and gene loss among the Laurasiatherian and Euarchontoglires species included in the study. Interestingly, cetaceans present an increased loss of hair-type keratin genes when compared to other terrestrial mammals. As suggested by the ‘less-is-more’ hypothesis, we do not rule out the possibility that the gene loss of hair-type keratin genes in these species might be associated to the hairless phenotype and could have been adaptive in response to new selective pressures imposed by the colonization of a new habitat. Our study provides support for the idea that pseudogenes are not simply ‘genomic fossils’ but instead have adaptive roles during the evolutionary process.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-869) contains supplementary material, which is available to authorized users.     

Evolution of the interleukin-1 gene family in mammals

The phylogeny of interleukin-1 family genes shows that human interleukin-1 (IL-1) is more closely related to IL-1 of the bovine than to IL-1 of the mouse, whereas human interleukin-1 (IL-1) is more closely related to IL-1 of the mouse than to IL-1 of the bovine. The IL-1 receptor antagonist (IL-1) shows homology to the C-terminal region of both IL-1 and IL-1. In the C-terminal region, the IL-1 genes of human and mouse have diverged more from each other at nonsynonymous sites than have either IL-1 or IL-1; because the same pattern is not seen at synonymous sites, it must be due not to a difference in mutation rate but rather to a greater degree of functional constraint on this region in the IL-1 and IL-1 proteins than in the IL-1 protein. But synonymous sites in IL-1 of mouse have evolved more rapidly than in IL-1 of human, indicating a higher rate of mutation in the former gene. In the N-terminal region of the protein, nonsynonymous sites have evolved at similar rates in IL-1 and IL-1. The first exon of the IL-1 gene, which encodes the leader peptide, shows evidence of homology with the first exon of IL-1, which is not translated. Thus, it seems likely that IL-1 evolved by duplication of an IL-1 gene and loss of expression of exons 2–4. Correspondence to: A.L. Hughes     

DNA methylation profiling of pseudogene-parental gene pairs and two gene families

A substantial proportion of human genes contain tissue-specifically DNA-methylated regions (TDMRs). However, little is known about the evolutionary conservation of differentially methylated loci, how they evolve, and the signals that regulate them. We have studied TDMR conservation in the PLG and TBX gene families and in 32 pseudogene–parental gene pairs. Among the members of the recently evolved PLG gene family, 5′-UTR methylation is conserved and inversely correlated with the cognate gene expression, indicating as well a conserved regulatory role of DNA methylation. Conversely, many genes of the much older TBX family display complementary tissue-specific methylation, suggesting an epigenetic complementation in the evolution of this gene family. Similar to gene families, unprocessed pseudogenes arose from gene duplications and we found TDMR conservation in some pseudogene–parental gene pairs displaying short evolutionary distances. However, for the majority of unprocessed pseudogenes and for all processed pseudogenes examined, we found that tissue-specific methylation arose de novo after gene duplication.     

Intragenomic Variation and Evolution of the Internal Transcribed Spacer of the rRNA Operon in Bacteria

Variation in the internal transcribed spacer (ITS) of the rRNA (rrn) operon is increasingly used to infer population-level diversity in bacterial communities. However, intragenomic ITS variation may skew diversity estimates that do not correct for multiple rrn operons within a genome. This study characterizes variation in ITS length, tRNA composition, and intragenomic nucleotide divergence across 155 Bacteria genomes. On average, these genomes encode 4.8 rrn operons (range: 2–15) and contain 2.4 unique ITS length variants (range: 1–12) and 2.8 unique sequence variants (range: 1–12). ITS variation stems primarily from differences in tRNA gene composition, with ITS regions containing tRNA-Ala + tRNA-Ile (48% of sequences), tRNA-Ala or tRNA-Ile (10%), tRNA-Glu (11%), other tRNAs (3%), or no tRNA genes (27%). Intragenomic divergence among paralogous ITS sequences grouped by tRNA composition ranges from 0% to 12.11% (mean: 0.94%). Low divergence values indicate extensive homogenization among ITS copies. In 78% of alignments, divergence is <1%, with 54% showing zero variation and 81% containing at least two identical sequences. ITS homogenization occurs over relatively long sequence tracts, frequently spanning the entire ITS, and is largely independent of the distance (basepairs) between operons. This study underscores the potential contribution of interoperon ITS variation to bacterial microdiversity studies, as well as unequivocally demonstrates the pervasiveness of concerted evolution in the rrn gene family. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Reviewing Editor: Dr. Margaret Riley     

Evolutionary Aspects of Functional and Pseudogene Members of the Phytochrome Gene Family in Scots Pine

According to the neutral theory of evolution, mutation and genetic drift are the only forces that shape unconstrained, neutral, gene evolution. Thus, pseudogenes (which often evolve neutrally) provide opportunities to obtain direct estimates of mutation rates that are not biased by selection, and gene families comprising functional and pseudogene members provide useful material for both estimating neutral mutation rates and identifying sites that appear to be under positive or negative selection pressures. Conifers could be very useful for such analyses since they have large and complex genomes. There is evidence that pseudogenes make significant contributions to the size and complexity of gene families in pines, although few studies have examined the composition and evolution of gene families in conifers. In this work, I examine the complexity and rates of mutation of the phytochrome gene family in Pinus sylvestris and show that it includes not only functional genes but also pseudogenes. As expected, the functional PHYO does not appear to have evolved neutrally, while phytochrome pseudogenes show signs of unconstrained evolution.     

A complex glutathione transferase gene family in the housefly Musca domestica

In most metazoans, the glutathione S-transferases (GST) are encoded by gene families, and are used to detoxify xenobiotics. We describe the structure of genomic loci coding for the GSTs in the housefly that have been implicated, by both genetic and biochemical means, in mediating insecticide resistance. In earlier work, we showed that one of the theta-class enzymes, MdGST-3, is overproduced in resistant flies and degrades certain insecticides. We used a fragment from a cDNA clone of MdGST-3 as a probe to screen a housefly genomic DNA bank in phage λ. This probe detected multiple gst loci. Genes for GSTs were found in five different, nonoverlapping λ clones, three of which carry multiple, closely linked gsts. Multiple genes for both MdGST-3 and MdGST-4 were found; some of which have introns in their 5′ untranslated regions. In adults, the only MdGST-3 enzymes that are expressed are encoded by the intron-free genes. A new theta-class GST (called MdGST-5) was also discovered. Fusion genes comprising 5′ MdGST-3 sequences and either MdGST-4 or MdGST-5 sequences in their 3′ halves were encountered at three separate loci. The genes described here are found in both the ancestral sensitive strain and the insecticide-resistant strains. Received: 28 June 1996 / Accepted: 23 April 1997     

Evolution of isozyme loci and their differential tissue expression

Summary The phylogeny of the creatine kinase (CK, EC 2.7.3.2) isozyme loci and their differential tissue expressions were determined for representatives of 65 families of vertebrates, with emphasis on the fishes. The transition from the single creatine kinase locus, characteristic of certain echinoderms, to the two creatine kinase loci which are orthologous to those present in all vertebrates, occurred early in the chordate line. The majority of pre-teleostean fishes possesses only these two CK loci (A and C). These loci are relatively generalized in their tissue expressions which are variable among species of primitive fishes. The third and fourth creatine kinase loci (B and D) arose separately in the ancestors of the bony fishes and appear to be the result of regional genome duplications. Concomitant with the increase in the number of isozyme loci has been an increase in the specificity of their tissue expression. In the advanced teleost fishes the four CK loci are differentially expressed in a characteristic manner. The A₂ isozyme predominates in skeletal muscle, the B₂ isozyme in eye and brain, the C₂ isozyme in stomach muscle, and the D₂ isozyme is found exclusively in testis. We propose a phylogeny of the creatine kinase genes in the lower chordates based on the time of appearance of new CK loci, the sequence in which the loci achieve a tissue restricted expression, and the immunochemical relatedness of the orthologous and paralogous gene products.     

Length Variation in 18S rRNA Expansion Segment 43/e4 of <Emphasis Type="Italic">Daphnia obtusa</Emphasis>: Ancient or Recurring Polymorphism?

Expansion segments in ribosomal DNA (rDNA) can show length variation at the level of the individual, yet our understanding of the evolutionary forces shaping this variation is incomplete. Previous studies of expansion segment 43/e4 of the 18S rRNA gene in Daphnia obtusa have examined this variation in six individuals; however, it is not known if the variation documented at this locus is representative of variation across the species’ geographic range. Furthermore, it is unclear whether length variants found in multiple individuals share common ancestry, or were generated de novo through recombination. We quantified expansion segment length variant frequencies in 134 individual D. obtusa from 33 populations at 15 sites across the species range in the US, and used a phylogeographic approach to determine whether recombination continues to add to the standing crop of variation at this locus. We identified seven length variants across the sampling range, which spans almost 3000 km. Based on the phylogeographic distribution of length variants in the expansion segment, we conclude that they are shared ancient polymorphisms that have persisted despite the operation of molecular mechanisms that cause the concerted evolution of multigene families such as rDNA. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Evolution of the mouse polyubiquitin-C gene

The polymeric ubiquitin (poly-u) genes are composed of tandem 228-bp repeats with no spacer sequences between individual monomer units. Ubiquitin is one of the most conserved proteins known to date, and the individual units within a number of poly-u genes are significantly more similar to each other than would be expected if each unit evolved independently. It has been proposed that the rather striking similarity among poly-u monomers in some lineages is caused by a series of homogenization events. Here we report the sequences of the polyubiquitin-C (Ubc) genes in two mouse strains. Analysis of these sequences, as well as those of the previously reported Chinese hamster and rat poly-u genes, supports the assertion that the homogenization of the ubiquitin-C gene in rodents is due to unequal crossing-over events. The sequence divergence of noncoding DNA was used to estimate the frequency of unequal crossing-over events (6.3 × 10⁻⁵ events per generation) in the Ubc gene, as well as to provide evidence of apparent selection in the poly-u gene.     

Evolution of the cyclin gene family in plants

Cyclins are key regulators of cell cycle progression. Previous studies have shown that cyclin genes in plants can be divided into 10 groups. However, because those studies only focused on genes from two well-known model plants (i.e., Arabidopsis thaliana (L.) Heynh. and Oryza sativa L.), it remains unclear whether the 10 groups are reasonably defined. In this study, by analyzing the genomes of 10 representative plants (Chlamydomonas reinhardtii P. A. Dang, Physcomitrella patens(Hedw.) Bruch & Schimp., Selaginella moellendorffii Hieron., Picea abies (L.) H. Karst., Amborella trichopoda Baill., A. thaliana, Populus trichocarpa Torr. & A. Gray ex Hook., Vitis vinifera L., O. sativa, and Sorghum bicolor (L.) Moench), we estimated the phylogenetic relationships of plant cyclins and investigated their evolutionary patterns. We confirmed that plant cyclins can be classified into 10 groups, although only eight ancestral genes may have existed in the most recent common ancestor of extant green plants. We also found that, due to the frequent occurrences of gene duplication events, several groups have expanded extensively in seed plants and, particularly, flowering plants, so that multiple genes belonging to different subgroups are present in a species. Reconciliation of the evolutionary histories of these groups and subgroups further led to the identification of evolutionarily highly conserved and rapidly duplicating gene lineages. These results will guide the classification and nomenclature of plant cyclins and help understand the conservativeness and variation in their functions.