The involucrin gene of the owl monkey: origin of the early region

A large part of the coding region of the hominoid involucrin gene is of recent origin. This part of the gene, which we have called the modern segment, contains numerous repeats of a sequence of 10 codons, created by multiple duplications some of which consist of 3-12 repeats. We have sequenced two alleles of the involucrin gene in the owl monkey and found that the involucrin gene of this species also possesses a modern segment. By comparing the modern segment of the owl monkey with that of the hominoids, we find that only a part of this segment is shared by the two species. We call this part the early region because it must have originated in a common ancestor of the anthropoids. The rest of the hominoid modern segment does not correspond to any groups of repeats in the owl monkey and was therefore created after divergence of the two lineages. As in the hominoids, the latest additions to the modern segment of the owl monkey have been in its 5' half, which possesses different duplication patterns in the two alleles. Lineage divergences within the anthropoids can be detected at different sites within the modern segment.      

Structure and evolution of the human involucrin gene

Involucrin is a keratinocyte protein that first appears in the cell cytosol, but ultimately becomes cross-linked to membrane proteins by transglutaminase. The gene for human involucrin has now been cloned and sequenced. The central segment of the coding region contains 39 repeats of a 30 nucleotide sequence whose ten encoded amino acids include three glutamines and two glutamic acids. This segment must have originated by successive duplications. Later duplications of modified sequences within the central segment can also be identified. Flanking the central segment lie shorter coding segments, a part of which must have given rise to the central segment. The flanking segments also show homology to a simpler 30 nucleotide sequence from which they likely originated. The evolution of involucrin as a substrate of transglutaminase and an envelope precursor was evidently made possible by this process of repeated mutation and duplication.     

The involucrin gene of the orangutan: generation of the late region as an evolutionary trend in the hominoids

In the evolutionary line leading to the higher primates, the coding region of the involucrin gene evolved a segment consisting of numerous repeats of a 10-codon sequence. Additions to this segment of repeats have been made successively, thus generating regions that can be defined as early, middle, and late. The involucrin gene of the orangutan (Pongo pygmaeus abelii) possesses a segment of repeats whose early region has the same repeat structure as that in other anthropoids. The middle region is not similar in repeat structure to that of all anthropoids but is similar to that of other hominoids. The late region is unique to the species; it does not correspond at all in its repeat structure to that of the human or gorilla and is much larger. The late region of the orangutan was generated by duplications of blocks of older repeats clearly belonging to the middle region. Continued duplications extending the late region are an evolutionary trend in the hominoids. The process of addition of repeats at a particular location is a more significant aspect of the evolution of involucrin than are random nucleotide substitutions; in addition, it has proceeded more rapidly.      

The involucrin genes of pig and dog: comparison of their segments of repeats with those of prosimians and higher primates

The involucrin genes of the dog and the pig have been cloned and sequenced. Like the corresponding genes of the prosimians, each contains a homologous segment of short tandem repeats at the same position in the coding region. However, the codon sequence of the repeats in the prosimians differs significantly from that of the nonprimate mammals. This evolution has been brought about by a combination of genetic modifications (selective deletions, mutations, and gene conversions). In the anthropoids, this segment of repeats was replaced by a modern one differing in location, sequence, and repeat length. In several of its properties the modern segment has continued the prosimian trend away from the nonprimates. The overall direction of the evolution of this segment has therefore been maintained even though there have been sudden changes in the evolutionary processes acting on the gene.     

The involucrin gene of Old-World monkeys and other higher primates: synapomorphies and parallelisms resulting from the same gene-altering mechanism.

The involucrin gene of platyrrhines and hominoids contains a segment of 10-codon repeats which were added vectorially at the same site in the coding region. We have now cloned and sequenced the involucrin gene of four cercopithecoid monkeys--two macaques (mulatta and fascicularis) and two Cercopithecus monkeys (aethiops and hamlyni). Each gene contains a similar segment of short repeats; some of these were added in a common anthropoid lineage, others were added in a common catarrhine lineage, and still others were added in a common macaque or Cercopithecus lineage. Repeats added before a lineage diverges become synapomorphies in the sister taxa resulting from the divergence. Repeats added independently in different diverged lineages become parallelisms. The synapomorphies are the result of the action of a targeted duplication mechanism acting in a common ancestral lineage, but the parallelisms are the result of the same duplication mechanism transmitted to successively divergent sublineages and acting independently in each.     

The involucrin gene of the galago. Existence of a correction process acting on its segment of repeats

The involucrin gene of the galago, a prosimian, has been cloned and sequenced. The coding region contains a segment of repeats homologous to the segment of repeats in the gene of another prosimian, the lemur, and different from the segments of repeats in the genes of higher primates. The repeats lengths in the two prosimians are similar; and except for a single duplication of a block of repeats in the lemur alone, the number of repeats is the same. However, the nucleotide consensus sequences of the repeats differ between the two species at 3 out of 39 nucleotide positions. The repeats therefore appear to have been modified by a correction process that led toward homogeneity in the repeats of each species while permitting divergence between the two species. The correction process, an example of concerted evolution, has taken place preferentially between adjacent repeats. The numerous differences between the segments of repeats of higher primates and the segments of repeats of lower animals reveal a discontinuity in the evolutionary processes acting on the gene.     

Remodeling of the involucrin gene during primate evolution

The protein involucrin is a product of terminal differentiation in the epidermal cell and related cell types. By comparing the nucleotide sequence of the involucrin gene of the lemur with that of the human, it is clear that the gene has undergone unusual evolution in the primates. The coding region of the gene contains an ancestral segment, most of which is common to the lemur and the human, and a species-specific segment of repeats derived from the ancestral segment. Instead of the modern segment of repeats found in the human gene, the lemur gene possesses repeats derived from another sequence at a different location in the ancestral segment. The two kinds of segments of repeats probably represent alternative ways of creating a repeat structure in the involucrin molecule. The modern segment of repeats must have been created after divergence of the higher primates from the prosimians.     

Consecutive actions of different gene-altering mechanisms in the evolution of involucrin.

During the evolution of primates from nonprimates, the gene for involucrin was greatly altered by changes in the short tandem repeats that are present in some form in the gene of each of 17 species examined. The evolution of involucrin was not the result of a single continuum of more or less random changes, and it was not confined to the process of nucleotide substitution, the most commonly studied evolutionary change in DNA. Instead, the evolution of this gene took place through different mechanisms that shortened the length of the repeats, increased their number, and changed their codon sequence. As part of this trend, one entire segment of repeats was replaced by another located elsewhere in the coding region. To bring about these changes, specific mechanisms have been activated, deactivated, and replaced by other mechanisms. The resulting serial revisions in the involucrin gene must depend on gene-altering machinery whose synthesis or activity can be controlled.     

Systematic repeat addition at a precise location in the coding region of the involucrin gene of wild mice reveals their phylogeny

The involucrin gene encodes a protein of terminally differentiated keratinocytes. Its segment of repeats, which represents up to 80% of the coding region, is highly polymorphic in mouse strains derived from wild progenitors. Polymorphism includes nucleotide substitutions, but is most strikingly due to the recent addition of a variable number of repeats at a precise location within the segment of repeats. Each mouse taxon examined showed consistent and distinctive patterns of evolution of its variable region: very rapid changes in most M. m. domesticus alleles, slow changes in M. m. musculus, and complete arrest in M. spretus. We conclude that changes in the variable region are controlled by the genetic background. One of the M. m. domesticus alleles (DIK-L), which is of M. m. musculus origin, has undergone a recent repeat duplication typical of M. m. domesticus. This suggests that the genetic background controls repeat duplications through trans-acting factors. Because the repeat pattern differs in closely related murine taxa, involucrin reveals with greater sensitivity than random nucleotide substitutions the evolutionary relations of the mouse and probably of all murids.     

A synthetic translation-terminator gene: A tool for dissecting the translation direction of a gene

A 41-nucleotide-long duplex DNA, which contains the translation termination codon TAA in six reading frames and lactose operator sequence of Escherichiacoli, has been synthesized. This fragment may be useful not only for producing a truncated protein encoded in a plasmid, but also for the identification of the precise coding region and translation direction of a bacterial gene in the cloned chromosomal segment. The synthetic fragment was inserted into ß-lactamase structural gene in pBR322 in order to test the in vivo activity. The plasmid produced mutant ß-lactamase reduced in size, as expected from the insertion site, and rendered the host bacterium constitutive for ß-galactosidase. Thus, termination codons and lactose operator in synthetic nucleotide appear to be functional in vivo.     

Gaining Insights into the Codon Usage Patterns of TP53 Gene across Eight Mammalian Species

TP53 gene is known as the “guardian of the genome” as it plays a vital role in regulating cell cycle, cell proliferation, DNA damage repair, initiation of programmed cell death and suppressing tumor growth. Non uniform usage of synonymous codons for a specific amino acid during translation of protein known as codon usage bias (CUB) is a unique property of the genome and shows species specific deviation. Analysis of codon usage bias with compositional dynamics of coding sequences has contributed to the better understanding of the molecular mechanism and the evolution of a particular gene. In this study, the complete nucleotide coding sequences of TP53 gene from eight different mammalian species were used for CUB analysis. Our results showed that the codon usage patterns in TP53 gene across different mammalian species has been influenced by GC bias particularly GC₃ and a moderate bias exists in the codon usage of TP53 gene. Moreover, we observed that nature has highly favored the most over represented codon CTG for leucine amino acid but selected against the ATA codon for isoleucine in TP53 gene across all mammalian species during the course of evolution.     

The involucrin genes of the mouse and the rat: study of their shared repeats

The involucrin genes of the mouse (Mus musculus) and the rat (Rattus norvegicus) have been cloned and sequenced. The coding region of each gene contains, at site P, a segment of repeats homologous to that of other nonanthropoid mammals. In contrast to the repeats of species belonging to different mammalian orders, many individual repeats of the mouse and the rat can be matched. Both before and after the divergence of the two species, these repeats have been the site of systematic alterations in nucleotide sequence. One of the alterations is the correction of nucleotides of one repeat by those of another. Corrected nucleotides may be closely linked to flanking nucleotides that are uncorrected; the systematic correction process therefore appears to be due to gene conversion. There is a stretch of 18 reiterated CAGs in the segment of repeats of the Mus gene; most of these reiterations were introduced recently, supporting the idea that the gene was generated originally from poly CAG. An antiserum to a synthetic peptide encoded by the segment of repeats of the Mus gene reveals differentiation- specific expression of the gene in the epidermis.      

Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene

The codon usage of the Angiosperm psbA gene is atypical for flowering plant chloroplast genes but similar to the codon usage observed in highly expressed plastid genes from some other Plantae, particularly Chlorobionta, lineages. The pattern of codon bias in these genes is suggestive of selection for a set of translationally optimal codons but the degree of bias towards these optimal codons is much weaker in the flowering plant psbA gene than in high expression plastid genes from lineages such as certain green algal groups. Two scenarios have been proposed to explain these observations. One is that the flowering plant psbA gene is currently under weak selective constraints for translation efficiency, the other is that there are no current selective constraints and we are observing the remnants of an ancestral codon adaptation that is decaying under mutational pressure. We test these two models using simulations studies that incorporate the context-dependent mutational properties of plant chloroplast DNA. We first reconstruct ancestral sequences and then simulate their evolution in the absence of selection on codon usage by using mutation dynamics estimated from intergenic regions. The results show that psbA has a significantly higher level of codon adaptation than expected while other chloroplast genes are within the range predicted by the simulations. These results suggest that there have been selective constraints on the codon usage of the flowering plant psbA gene during Angiosperm evolution.     

Molecular cloning and sequence analysis of the ribosomal ‘A’ protein gene from the archaebacterium,Halobacterium halobium

The ribosomal ‘A’ protein gene of Halobacterium halobium has been cloned and the nucleotide sequence of the DNA fragment containing the ‘A’ protein gene has been determined. The amino-acid sequence of the protein deduced from the nucleotide sequence was established from manual sequence analysis of the protein and structural data provided by peptides derived from cleavage of the protein with various proteinases. The ‘A’ protein consisted of 114 amino acids with a molecular weight of 11562 and was characterized mainly by a high amounts of alanine and acidic amino acid in the C-terminal half of the molecule. The coding sequence of the gene was preceded by a predicted Shine-Dalgarno sequence and two terminal codons. There was no intron or insertion sequence in the coding sequence. Following the terminal codon of the ‘A’ gene, there was a structure reminiscent of the Escherichia coli rho-independent terminator. The G + C content of the coding sequence was found to be 71%. Inspection of the codon usage for the ‘A’ gene revealed 85% preference for G or C at the third codon position.     

The involucrin genes of the white-fronted capuchin and cottontop tamarin: the platyrrhine middle region.

In all anthropoid species, the coding region of the involucrin gene contains a segment of short tandem repeats that were added sequentially, beginning in a common anthropoid ancestor. The involucrin coding region of each of two platyrrhine species, the white-fronted capuchin (Cebus albifrons) and the cottontop tamarin (Saguinus oedipus), has now been cloned and sequenced. These genes share with the genes of the catarrhines the repeats added in the common anthropoid lineage (the early region). After their divergence, the platyrrhines, like the catarrhines, continued to add repeats vectorially 5' of the early region, to form a middle region. The mechanism that was established in the common anthropoid lineage for the addition of repeats at a definite site in the coding region was transmitted to both platyrrhines and catarrhines, enabling each to generate its middle region independently. The process of vectorial repeat addition continued in two platyrrhine sublineages after their divergence from each other.     

Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis

Patterns of codon usage have been extensively studied among Bacteria and Eukaryotes, but there has been little investigation of species from the third domain of life, the Archaea. Here, we examine the nature of codon usage bias in a methanogenic archaeon, Methanococcus maripaludis. Genome-wide patterns of codon usage are dominated by a strong A + T bias, presumably largely reflecting mutation patterns. Nevertheless, there is variation among genes in the use of a subset of putatively translationally optimal codons, which is strongly correlated with gene expression level. In comparison with Bacteria such as Escherichia coli, the strength of selected codon usage bias in highly expressed genes in M. maripaludis seems surprisingly high given its moderate growth rate. However, the pattern of selected codon usage differs between M. maripaludis and E. coli: in the archaeon, strongly selected codon usage bias is largely restricted to twofold degenerate amino acids (AAs). Weaker bias among the codons for fourfold degenerate AAs is consistent with the small number of tRNA genes in the M. maripaludis genome.     

Cytochrome oxidase subunit II gene in mitochondria of Oenothera has no intron

The cytochrome oxidase subunit II gene has been localized in the mitochondrial genome of Oenothera berteriana and the nucleotide sequence has been determined. The coding sequence contains 777 bp and, unlike the corresponding gene in Zea mays, is not interrupted by an intron. No TGA codon is found within the open reading frame. The codon CGG, as in the maize gene, is used in place of tryptophan codons of corresponding genes in other organisms. At position 742 in the Oenothera sequence the TGG of maize is changed into a CGG codon, where Trp is conserved as the amino acid in other organisms. Homologous sequences occur more than once in the mitochondrial genome as several mitochondrial DNA species hybridize with DNA probes of the cytochrome oxidase subunit II gene.     

Complete mitochondrial genome of Dacus conopsoides (Insecta: Tephritidae) with tRNA gene duplication and molecular phylogeny of Dacini tribe

To date there is only a single report on the complete mitochondrial genome of the Dacus fruit flies. We report here the whole mitogenome of Dacus conopsoides with first report of tRNA gene duplication in tephritid fruit flies determined using next-generation sequencing and discuss the molecular phylogeny of Dacini tribe. It had a total length of 15,852 bp, comprising 13 protein coding genes, 2 rRNA genes, 23 tRNA genes, and a non-coding region (A + T-rich control region). The 65-bp trnF gene was duplicated, and the 68-bp trnE gene was partially duplicated resulting in a 31-bp pseudogene. The cloverleaf structure for trnN, trnH, and trnF lacked the TΨC-loop, while trnS lacked the D-stem. The start codons for the protein coding genes included 6 ATG, 3 ATC, 2 ATA, and 1 each of ATT and TCG. Seven PCGs had TAA stop codon, two had TAG and four had incomplete T stop codon. Molecular phylogeny based on 15 mt-genes (13 PCGs +2 rRNA genes) and 30 taxa of Tephritidae indicated D. conopsoides forming a monophyletic sister group with D. longicornis supported by high bootstrap value. The lineage containing also the monophyletic genus Zeugodacus. The Dacini and Ceratitidini tribes of the subfamily Dacinae were monophyletic but the subfamilies Dacinae and Trypetinae were paraphyletic. A broader taxa sampling of the Tephritidae is needed to better elucidate the phylogenetics and systematics of the tribes and subfamilies of tephritid fruit flies.