Evidence against the exon theory of genes derived from the triose-phosphate isomerase gene

Evolutionary dynamics of triosephosphate isomerase gene intron location pattern in Metazoa: A new perspective on intron evolution in animals

Intron evolution, including its dynamics in the evolutionary transitions and diversification of eukaryotes, remains elusive. Inadequate taxon sampling due to data shortage, unclear phylogenetic framework, and inappropriate outgroup application might be among the causes. Besides, the integrity of all the introns within a gene was often neglected previously. Taking advantage of the ancient conserved triosephosphate isomerase gene (tim), the relatively robust phylogeny of Metazoa, and choanoflagellates as outgroup, the evolutionary dynamics of tim intron location pattern (ILP) in Metazoa was investigated. From 133 representative species of ten phyla, 30 types of ILPs were identified. A most common one, which harbors the maximum six intron positions, is deduced to be the common ancestral tim ILP of Metazoa, which almost had formed in their protozoan ancestor and was surprisingly retained and passed down till to each ancestors of metazoan phyla. In the subsequent animal diversification, it underwent different evolutionary trajectories: within Deuterostomia, it was almost completely retained only with changes in a few species with relatively recently fast-evolving histories, while within the rapidly radiating Protostomia, besides few but remarkable retention, it usually displayed extensive intron losses and a few gains. Therefore, a common ancestral exon-intron arrangement pattern of an animal gene is definitely discovered; besides the 'intron-rich view' of early animal genes being confirmed, the novel insight that high exon-intron re-arrangements of genes seem to be associated with the relatively recently rapid evolution of lineages/species/genomes but have no correlation with the ancient major evolutionary transitions in animal evolution, is revealed.

Trichinella pseudospiralis vs. T. spiralis thymidylate synthase gene structure and T. pseudospiralis thymidylate synthase retrogene sequence

Background

Thymidylate synthase is a housekeeping gene, designated ancient due to its role in DNA synthesis and ubiquitous phyletic distribution. The genomic sequences were characterized coding for thymidylate synthase in two species of the genus Trichinella, an encapsulating T. spiralis and a non-encapsulating T. pseudospiralis.

Methods

Based on the sequence of parasitic nematode Trichinella spiralis thymidylate synthase cDNA, PCR techniques were employed.

Results

Each of the respective gene structures encompassed 6 exons and 5 introns located in conserved sites. Comparison with the corresponding gene structures of other eukaryotic species revealed lack of common introns that would be shared among selected fungi, nematodes, mammals and plants. The two deduced amino acid sequences were 96% identical. In addition to the thymidylate synthase gene, the intron-less retrocopy, i.e. a processed pseudogene, with sequence identical to the T. spiralis gene coding region, was found to be present within the T. pseudospiralis genome. This pseudogene, instead of the gene, was confirmed by RT-PCR to be expressed in the parasite muscle larvae.

Conclusions

Intron load, as well as distribution of exon and intron phases in thymidylate synthase genes from various sources, point against the theory of gene assembly by the primordial exon shuffling and support the theory of evolutionary late intron insertion into spliceosomal genes. Thymidylate synthase pseudogene expressed in T. pseudospiralis muscle larvae is designated a retrogene.

The evolution of spliceosomal introns: patterns, puzzles and progress

The origins and importance of spliceosomal introns comprise one of the longest-abiding mysteries of molecular evolution. Considerable debate remains over several aspects of the evolution of spliceosomal introns, including the timing of intron origin and proliferation, the mechanisms by which introns are lost and gained, and the forces that have shaped intron evolution. Recent important progress has been made in each of these areas. Patterns of intron-position correspondence between widely diverged eukaryotic species have provided insights into the origins of the vast differences in intron number between eukaryotic species, and studies of specific cases of intron loss and gain have led to progress in understanding the underlying molecular mechanisms and the forces that control intron evolution.

Phylogenetic and exon-intron structure analysis of fungal subtilisins: support for a mixed model of intron evolution

Phylogenetic and exon-intron structure analyses of intra- and interspecific fungal subtilisins in this study provided support for a mixed model of intron evolution: a synthetic theory of introns-early and introns-late speculations. Intraspecifically, there were three phase zero introns in Pr1A and its introns 1 and 2 located at the highly conserved positions were phylogentically congruent with coding region, which is in favor of the view of introns-early speculation, while intron 3 had two different sizes and was evolutionarily incongruent with coding region, the evidence for introns-late speculation. Noticeably, the subtilisin Pr1J gene from different strains of M. ansiopliae contained different number of introns, the strong evidence in support of introns-late theory. Interspecifically, phylogenetic analysis of 60 retrievable fungal subtilisins provided a clear relationship between amino acid sequence and gene exon-intron structure that the homogeneous sequences usually have a similar exon-infron structure. There were 10 intron positions inserted by highly biased phase zero introns across examined fungal subtilisin genes, half of these positions were highly conserved, while the others were species-specific, appearing to be of recent origins due to intron insertion, in favor of the introns-late theory. High conservations of positions 1 and 2 inserted by the high percentage of phase zero introns as well as the evidence of phylogenetic congruence between the evolutionary histories of intron sequences and coding region suggested that the introns at these two positions were primordial.

Rates of intron loss and gain: implications for early eukaryotic evolution

We study the intron-exon structures of 684 groups of orthologs from seven diverse eukaryotic genomes and provide maximum likelihood estimates for rates and numbers of intron losses and gains in these same genes for a variety of lineages. Rates of intron loss vary from approximately 2 x 10(-9) to 2 x 10(-10) per year. Rates of gain vary from 6 x 10(-13) to 4 x 10(-12) per possible intron insertion site per year. There is an inverse correspondence between rates of intron loss and gain, leading to a 20-fold variation among lineages in the ratio of the rates of the two processes. The observed rates of intron gain are insufficient to explain the large number of introns estimated to have been present in the plant-animal ancestor, suggesting that introns present in early eukaryotes may have been created by a fundamentally different process than more recently gained introns.

The structure of the juvenile hormone binding protein gene from Galleria mellonella

Juvenile hormone (JH) and ecdysone are the key hormones controlling insect growth and development. The juvenile hormone binding protein (JHBP) is the first member in the array of proteins participating in JH signal transmission. In the present report a wholejhbpgene sequence (9790 bp) is described. Thejhbpgene contains four introns (A–D). All the introns have common flanking sequences: GT at the 5′ and AG at the 3′ end. The first intron is in phase 1, the second in phase 2, and the third and fourth in phase 1. An analysis of these sequences suggests that U2-class spliceosomes are involved in intron excision from pre-mRNA. Several horizontally transmitted elements from other genes were found in the introns. Alljhbpexons are positioned in local AT-reach regions of the gene. A search for core promoter regulatory elements revealed that the TATA box starts 29 bp preceding the start of transcription; the sequence TCAGTA representing a putative initiator sequence (Inr) starts at position +14. Eight characteristic sequences for bindingBroad-Complexgene products, which coordinate the ecdysone temporal response, are present in the non-coding sequence of thejhbpgene. An analysis of exon locations and intron phases indicates thatjhbpgene organization is related to theretinol binding proteingene, a member of the lipocalin family.

Fractal properties of the human genome

The fractal dimension of the human chromosomes and four other genomes were determined using the box counting method. Human chromosomes exhibited a fractal dimension (D) of about 0.8, while values for a bacteria, yeast, worm and plant were higher. Analysis of three human chromosomes over five orders of magnitude of scale (from 10(8) to 10(4) bp), showed D to be non-constant at the smaller scales, when introns were included as gaps. The relationship between D and gene density fit an empirical equation related to that expected from theory, and allowed for the calculation of the fractal initiator or self-similarity ratio. This value (0.57) was constant at all scales for human chromosomes, and was similar for other species, except for Arabidopsis.

Proteomic identification, nucleotide sequence, heterologous expression and immunological reactivity of the triosephosphate isomerase of Paracoccidioides brasiliensis

An antigen of Paracoccidioides brasiliensis (Pb) was gel isolated and characterized. Endoproteinase Lys-C-digested peptides of the purified protein, which presented a molecular mass of 29 kDa and pI of 5.8, were subjected to sequence analysis of their amino acids. Searches at databases comparing the sequence of amino acids from the three peptides of the native protein revealed strong homology to triosephosphate isomerase (TPI: E.C. 5.3.1.1) from several sources. The complete cDNA and gene encoding PbTPI were obtained and both contained an open reading frame predicted to encode a 249-amino acid protein that presented all the peptides characterized in the native PbTPI. The Pbtpi gene contained six exons interrupted by five introns. Analysis performed with the deduced PbTPI suggested its usefulness in providing phylogenetic relatedness, as well as evidencing the correlation between the phylogeny provided by the deduced protein and intron positions in the cognate genes. The immunological reactivity of PbTPI was examined. The complete coding cDNA of PbTPI was overexpressed in an Escherichia coli host to produce high levels of recombinant fusion protein with glutathione S-transferase (GST) that had been purified by affinity chromatography. The purified recombinant TPI was recognized by sera of patients with confirmed paracoccidioidomycosis and not by sera of healthy individuals. Thus, recombinant PbTPI can be a valuable addition to the still small arsenal of P. brasiliensis immunoreactive proteins, which could be tested for incorporation into assays for serodiagnosis of the disease.

A genomic BAC library and a new BAC-GFP vector to study the holocentric pest Spodoptera frugiperda

Two genomic tools for the study of Lepidoptera and the holocentric structure of their chromosomes are presented in this paper. A bacterial artificial chromosome (BAC) library was constructed using nuclear DNA partially digested with HindIII from eggs of Spodoptera frugiperda. The library contains a total of 36,864 clones with an average insert size of 125 kb, which corresponds to approximately 11.5 genome equivalents. Hybridization screening of the library was performed with eight single-copy genes, giving an average hit of 10 clones per marker gene. Colinearity between the genome and BACs was demonstrated at the triose phosphate isomerase (tpi) locus. Probing of the library with a PCR fragment internal to the 18S ribosomal gene allowed an estimation of the rDNA locus size close to 115 repeats per haploid genome. A new vector (pBAC3.6eGFP) for transient transfection into S. frugiperda cell lines has been constructed. It is based on the BAC vector, pBAC3.6e, in which a gene encoding GFP was inserted under the control of the densovirus P9 promoter. This vector has the advantage to accommodate large genomic inserts and to be transfected in a large lepidopteran host range. It was used to construct a second BAC library from Sf9 cell nuclear DNA in order to allow a comparison between somatic and cell line genome organization.

Recent Intron Gain in Elongation Factor-1α of Colletid Bees (Hymenoptera: Colletidae)

We discovered the presence of a unique spliceosomal intron in the F1 copy of elongation factor-1alpha (EF-1alpha) restricted to the bee family Colletidae (Hymenoptera: Apoidae). The intron ranges in size from 101 to 1044 bp and shows no positional sliding. Our data also demonstrate the complete absence of this intron from exemplars representing all other bee families, as well as from close hymenopteran relatives. A review of the literature finds that this intron is likewise absent from all other arthropods for which data are available. This provides unambiguous evidence for a relatively recent intron insertion event in the colletid common ancestor and, at least in this specific instance, lends support to the introns-late hypothesis. The comparative distribution of this novel intron also supports the monophyly of Colletidae and the exclusion of the Stenotritidae from this family, providing an example of the potential of some introns to act as robust markers of shared descent.

A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae)

While Anartia butterflies have served as model organisms for research on the genetics of speciation, no phylogeny has been published to describe interspecific relationships. Here, we present a molecular phylogenetic analysis of Anartia species relationships, using both mitochondrial and nuclear genes. Analyses of both data sets confirm earlier predictions of sister species pairings based primarily on genital morphology. Yet both the mitochondrial and nuclear gene phylogenies demonstrate that Anartia jatrophae is not sister to all other Anartia species, but rather that it is sister to the Anartia fatima-Anartia amathea lineage. Traditional biogeographic explanations for speciation across the genus relied on A. jatrophae being sister to its congeners. These explanations invoked allopatric divergence of sister species pairs and multiple sympatric speciation events to explain why A. jatrophae flies alongside all its congeners. The molecular phylogenies are more consistent with lineage divergence due to vicariance, and range expansion of A. jatrophae to explain its sympatry with congeners. Further interpretations of the tree topologies also suggest how morphological evolution and eco-geographic adaptation may have set species range boundaries.

Differential partitioning of maternal fatty acid and phospholipid in neonate mosquito larvae

In animals, lipids are a source of energy, cell membrane components,signaling pathway modulators and emulsifying agents. In egg-laying animals,maternal yolk lipids, imported into the egg before laying, are metabolized or distributed in the developing embryo to serve these functions. Studies with birds, reptiles and insects have described lipid metabolism in adults and in eggs, but no studies have addressed how lipids are distributed in developing organs in the embryo. Here we show that maternal fatty acid and phospholipids segregate differently in tissues of newly hatched mosquito larvae. In the mother, both lipids are colocalized in yolk granules of developing oocytes and distributed evenly. In neonate larvae, however, the maternal fatty acid is stored along the side of the body, especially at the base of the body hair,and in the thorax, where the muscles are located, probably to provide energy for the rapid movements needed to find food immediately after birth. Most maternal phospholipids, however, are concentrated in the motile intestinal gastric caeca, from which they are released into the gut lumen where they may act as emulsifiers, probably to facilitate assimilation of the food the neonate ingests. Similar phenomena were observed in both Anopheles gambiae and Aedes aegypti mosquitoes, suggesting that such differential segregation of lipids is common to both insects. This study may lead to improved delivery of larvicidal agents and to efficient killing of newly hatched mosquito larvae as a control strategy for mosquito-borne diseases.

Split gene origin and periodic introns

The introns-early view has been challenged for several genes; prominent instances are triose phosphate isomerase (TPI), aldolase, pyruvate kinase (PK), alcohol dehydrogenase (ADH), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and myosin heavy chain. While some of their introns appear to be phylogenetically ancient and/or to delineate exons corresponding to protein modules, a considerable number seemingly do not. But it is argued here that many of these anomalous introns are periodic, that is, relics of internal sequence repetitions within the ancestral gene. Some of these periodic-intron patterns are shared between related genes, as in the alphabeta -barrels of TPI, aldolase and PK, or the Rossmann nucleotide-binding domain common to PK, ADH and GAPDH. This is further evidence for the ancestral status of these introns. The myosin heavy chain C-terminal rod region is paradoxical in that its sequence is clearly periodic but its intron placements are not; however, they exhibit a remarkable coherence of intron translational phases, suggesting that these introns may also have originally had a periodic arrangement now obscured by intron slipping.

The current state of insect molecular systematics: a thriving Tower of Babel

Insect molecular systematics has undergone remarkable recent growth. Advances in methods of data generation and analysis have led to the accumulation of large amounts of DNA sequence data from most major insect groups. In addition to reviewing theoretical and methodological advances, we have compiled information on the taxa and regions sequenced from all available phylogenetic studies of insects. It is evident that investigators have not usually coordinated their efforts. The genes and regions that have been sequenced differ substantially among studies and the whole of our efforts is thus little greater than the sum of its parts. The cytochrome oxidase I, 16S, 18S, and elongation factor-1 alpha genes have been widely used and are informative across a broad range of divergences in insects. We advocate their use as standards for insect phylogenetics. Insect molecular systematics has complemented and enhanced the value of morphological and ecological data, making substantial contributions to evolutionary biology in the process. A more coordinated approach focused on gathering homologous sequence data will greatly facilitate such efforts.

The recent origins of spliceosomal introns revisited

Does the intron/exon structure of eukaryotic genes belie their ancient assembly by exon-shuffling or have introns been inserted into preformed genes during eukaryotic evolution? These are the central questions in the ongoing 'introns-early' versus 'introns-late' controversy. The phylogenetic distribution of spliceosomal introns continues to strongly favor the intronslate theory. The introns-early theory, however, has claimed support from intron phase and protein structure correlations.

Molecular evolution: recent cases of spliceosomal intron gain?

The 'introns-late' theory holds that spliceosomal introns have been added to genes during eukaryotic evolution. Few clear examples of recent intron gains have been well documented, but two such cases have now been reported, one with possible identification of the source of the intron.

Intron loss and gain during evolution of the catalase gene family in angiosperms

Angiosperms (flowering plants), including both monocots and dicots, contain small catalase gene families. In the dicot, Arabidopsis thaliana, two catalase (CAT) genes, CAT1 and CAT3, are tightly linked on chromosome 1 and a third, CAT2, which is more similar to CAT1 than to CAT3, is unlinked on chromosome 4. Comparison of positions and numbers of introns among 13 angiosperm catalase genomic sequences indicates that intron positions are conserved, and suggests that an ancestral catalase gene common to monocots and dicots contained seven introns. Arabidopsis CAT2 has seven introns; both CAT1 and CAT3 have six introns in positions conserved with CAT2, but each has lost a different intron. We suggest the following sequence of events during the evolution of the Arabidopsis catalase gene family. An initial duplication of an ancestral catalase gene gave rise to CAT3 and CAT1. CAT1 then served as the template for a second duplication, yielding CAT2. Intron losses from CAT1 and CAT3 followed these duplications. One subclade of monocot catalases has lost all but the 5'-most and 3'-most introns, which is consistent with a mechanism of intron loss by replacement of an ancestral intron-containing gene with a reverse-transcribed DNA copy of a fully spliced mRNA. Following this event of concerted intron loss, the Oryza sativa (rice, a monocot) CAT1 lineage acquired an intron in a novel position, consistent with a mechanism of intron gain at proto-splice sites.

Genomic organization of the flt-1 gene encoding for vascular endothelial growth factor (VEGF) receptor-1 suggests an intimate evolutionary relationship between the 7-Ig and the 5-Ig tyrosine kinase receptors

The flt-1 tyrosine kinase gene encodes a high affinity receptor for Vascular Endothelial Growth Factor, and belongs to the so-called '7-Ig' or flt gene family which has characteristics of 7-Immunoglobulin (Ig)-like domains in the extracellular region. This is structurally distantly related to 5-Ig domain-containing receptors such as Fms/Kit/PDGF-R. However, the whole genomic organization for any 7-Ig receptor gene has not been determined yet. To examine the genomic structure of flt-1 and the evolutionary relationship between genes of the 7-Ig and 5-Ig receptor families, we isolated the mouse genomic DNAs carrying all exons of the flt-1 gene. The mouse flt-1 gene consisted of 30 exons, whose exon-intron boundaries were highly related to those in the 5-Ig receptor genes, except for the amino terminal region. The sequences corresponding to the first and second Ig-domains in the flt-1 gene were encoded by four exons, whereas this region was encoded by only two exons in the 5-Ig receptor genes. These results raise the interesting possibility that deletion or insertion mutations of introns in one of these receptor genes took place in the evolutionary generation of the other receptor genes.

New Drosophila introns originate by duplication

We have analyzed the phylogenetic distribution of introns in the gene coding for xanthine dehydrogenase in 37 species, including 31 dipterans sequenced by us. We have discovered three narrowly distributed novel introns, one in the medfly Ceratitis capitata, the second in the willistoni and saltans groups of Drosophila, and the third in two sibling species of the willistoni group. The phylogenetic distribution of these introns favors the "introns-late" theory of the origin of genes. Analysis of the nucleotide sequences indicates that all three introns have arisen by duplication of a preexisting intron, which is pervasive in Drosophila and other dipterans (and has a homologous position as an intron found in humans and other diverse organisms).

De novo insertion of an intron into the mammalian sex determining gene, SRY

Two theories have been proposed to explain the evolution of introns within eukaryotic genes. The introns early theory, or "exon theory of genes," proposes that introns are ancient and that recombination within introns provided new exon structure, and thus new genes. The introns late theory, or "insertional theory of introns," proposes that ancient genes existed as uninterrupted exons and that introns have been introduced during the course of evolution. There is still controversy as to how intron-exon structure evolved and whether the majority of introns are ancient or novel. Although there is extensive evidence in support of the introns early theory, phylogenetic comparisons of several genes indicate recent gain and loss of introns within these genes. However, no example has been shown of a protein coding gene, intronless in its ancestral form, which has acquired an intron in a derived form. The mammalian sex determining gene, SRY, is intronless in all mammals studied to date, as is the gene from which it recently evolved. However, we report here comparisons of genomic and cDNA sequences that now provide evidence of a de novo insertion of an intron into the SRY gene of dasyurid marsupials. This recently (approximately 45 million years ago) inserted sequence is not homologous with known transposable elements. Our data demonstrate that introns may be inserted as spliced units within a developmentally crucial gene without disrupting its function.

Genomic structure of TBX2 indicates conservation with distantly related T-box genes

TBX2 is a member of a recently discovered gene family of transcription factors, named T-box genes after the Brachyury or T gene. Mutations in two of these family members, TBX5 and TBX3, have recently been shown to be responsible for the congenital abnormalities associated with Holt Oram syndrome and ulnar-mammary syndrome respectively, while mutations in T-box genes in other species also result in developmental abnormalities in the tissues where the gene is normally expressed. Thus, it likely that other T-box genes are responsible for additional human developmental anomalies. Here we report the exon/intron boundaries of TBX2 and a polymorphism within intron 2 of TBX2 that should be useful for exploring the involvement of this gene in human genetic disease. We further note that the exon/intron boundaries of TBX2 are highly conserved within the T-box domain with those of both T and TBX5, as well as with a new human T-box gene and more distantly related genes from Caenorhabditis elegans and Drosophila. This observation should facilitate the analysis of the genomic structure of other members of this gene family. It is also of interest that several members of this gene family have an additional intron that is variably present within members of at least two different lineages of the T-box family. This observation has implications regarding the evolution of T-box genes.

Towards a reconciliation of the introns early or late views: triosephosphate isomerase genes from insects

The gene encoding the glycolytic enzyme, triosephosphate isomerase (TPI; EC 5.3.1.1), is a favourite model for molecular evolutionists who either subscribe to the theory that introns co-evolved with the ancestral gene, the introns early view, or alternatively, that introns are more recent immigrants. The discovery of an intron in the TPI gene of Culex mosquitoes at a site which was predicted by proponents of the intron early school supported that theory. More recently, the discovery of additional intron sites in several eukaryotes was presented as evidence supporting the introns late school. We have found the 'Culex intron' in two closely related mosquitoes, but not in two more evolutionary primitive Dipterans, suggesting that, if it is an 'ancient intron', loss may be more frequent than that supposed by the intron late school. In addition, we have found that three introns punctuating the TPI gene from the Lepidopteran, Heliothis, appear to be ancestrally related and may be the result of transposable element insertion, 50-90 million years ago. It is argued that both opposing schools in the intron debate be reconciled -- some introns may have been early and certainly others have arrived subsequent to the appearance of the TPI gene.

Exon/intron structure of aldehyde dehydrogenase genes supports the "introns-late" theory

Whether or not nuclear introns predate the divergence of bacteria and eukaryotes is the central argument between the proponents of the "introns-early" and "introns-late" theories. In this study we compared the goodness-of-fit of each theory with a probabilistic model of exon/intron evolution and multiple nonallelic genes encoding human aldehyde dehydrogenases (ALDHs). Using a reconstructed phylogenetic tree of ALDH genes, we computed the likelihood of obtaining the present-day ALDH sequences under the assumptions of each competing theory. Although on the grounds of its own assumptions each theory accounted for the ALDH data significantly better than its rival, the introns-early model required frequent intron slippage, and the estimated slippage rates were too high to be consistent with reported correlations between the boundaries of ancient protein modules and the ends of ancient exons. Because the molecular mechanisms proposed to explain intron slippage are incapable of providing such high rates and are incompatible with the observed distribution of introns in higher eukaryotes, the ALDH data support the introns-late theory.

Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination

The detailed genomic organization of a gene-dense region at human chromosome 12p13, spanning 223 kb of contiguous sequence, was determined. This region is composed of 20 genes and several other expressed sequences. Experimental tools including RT-PCR and cDNA sequencing, combined with gene prediction programs, were utilized in the analysis of the sequence. Various computer software programs were employed for sequence similarity searches and functional predictions. The high number of genes with diverse functions and complex transcriptional patterns make this region ideal for addressing challenges of gene discovery and genomic characterization amenable to large-scale sequence analysis.

Evidence that eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin

We have cloned and sequenced genes for triosephosphate isomerase (TPI) from the gamma-proteobacterium Francisella tularensis, the green non-sulfur bacterium Chloroflexus aurantiacus, and the alpha-proteobacterium Rhizobium etli and used these in phylogenetic analysis with TPI sequences from other members of the Bacteria, Archaea, and Eukarya. These analyses show that eukaryotic TPI genes are most closely related to the homologue from the alpha-proteobacterium and most distantly related to archaebacterial homologues. This relationship suggests that the TPI genes present in modern eukaryotic genomes were derived from an alpha-proteobacterial genome (possibly that of the protomitochondrial endosymbiont) after the divergence of Archaea and Eukarya. Among these eukaryotic genes are some from deeply branching, amitochondrial eukaryotes (namely Giardia), which further suggests that this event took place quite early in eukaryotic evolution.

Intron positions correlate with module boundaries in ancient proteins

We analyze the three-dimensional structure of proteins by a computer program that finds regions of sequence that contain module boundaries, defining a module as a segment of polypeptide chain bounded in space by a specific given distance. The program defines a set of "linker regions" that have the property that if an intron were to be placed into each linker region, the protein would be dissected into a set of modules all less than the specified diameter. We test a set of 32 proteins, all of ancient origin, and a corresponding set of 570 intron positions, to ask if there is a statistically significant excess of intron positions within the linker regions. For 28-A modules, a standard size used historically, we find such an excess, with P < 0.003. This correlation is neither due to a compositional or sequence bias in the linker regions nor to a surface bias in intron positions. Furthermore, a subset of 20 introns, which can be putatively identified as old, lies even more explicitly within the linker regions, with P < 0.0003. Thus, there is a strong correlation between intron positions and three-dimensional structural elements of ancient proteins as expected by the introns-early approach. We then study a range of module diameters and show that, as the diameter varies, significant peaks of correlation appear for module diameters centered at 21.7, 27.6, and 32.9 A. These preferred module diameters roughly correspond to predicted exon sizes of 15, 22, and 30 residues. Thus, there are significant correlations between introns, modules, and a quantized pattern of the lengths of polypeptide chains, which is the prediction of the "Exon Theory of Genes."

A difficult phase for introns-early. Molecular evolution

Close analysis of intron phase - the position of introns within codons - is claimed to provide novel evidence supporting the view that introns predate the divergence of bacteria and eukaryotes and, via 'exon shuffling', played a crucial role in protein evolution. But just how compelling is this evidence?

Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory

The gene encoding the glycolytic enzyme triose-phosphate isomerase (TPI; EC 5.3.1.1) has been central to the long-standing controversy on the origin and evolutionary significance of spliceosomal introns by virtue of its pivotal support for the introns-early view, or exon theory of genes. Putative correlations between intron positions and TPI protein structure have led to the conjecture that the gene was assembled by exon shuffling, and five TPI intron positions are old by the criterion of being conserved between animals and plants. We have sequenced TPI genes from three diverse eukaryotes--the basidiomycete Coprinus cinereus, the nematode Caenorhabditis elegans, and the insect Heliothis virescens--and have found introns at seven novel positions that disrupt previously recognized gene/protein structure correlations. The set of 21 TPI introns now known is consistent with a random model of intron insertion. Twelve of the 21 TPI introns appear to be of recent origin since each is present in but a single examined species. These results, together with their implication that as more TPI genes are sequenced more intron positions will be found, render TPI untenable as a paradigm for the introns-early theory and, instead, support the introns-late view that spliceosomal introns have been inserted into preexisting genes during eukaryotic evolution.