Structure and evolution of the apolipoprotein multigene family

Transcriptional and posttranscriptional regulation of apolipoprotein E, A-I, and A-II gene expression in normal rat liver and during several pathophysiologic states

Assessment of the relative transcription rates and mRNA steady-state levels for apolipoprotein genes E, A-I, and A-II has been performed in normal rat liver, during liver regeneration and following induction of cirrhosis, as well as in rats with inherited analbuminemia associated with hyperlipidemia. Apo E exhibits primarily transcriptional control with an additional component of posttranscriptional control, whereas Apo A-I is controlled primarily at the posttranscriptional level, thus indicating that these genes are regulated independently. The level of control for Apo A-II has not been determined, because of difficulty experienced in measuring the transcription rate of this gene. During liver regeneration, cirrhosis, and analbuminemia, there is a marked increase in the ratio of Apo A-I to Apo E mRNA, resulting from an increase in the Apo A-I mRNA steady-state level and a decrease in Apo E mRNA. These changes are similar in the three pathophysiologic states and seem to occur through a combination of transcriptional and posttranscriptional mechanisms.

Codon usage changes and sequence dissimilarity between human and rat

This paper reports on the relationship between the number of silent differences and the codon usage changes in the lineages leading to human and rat. Examination of 102 pairs of homologous genes gives rise to four main conclusions: (1) We have previously demonstrated the existence of a codon usage change (called the minor shift) between human and rat; this was confirmed here with a larger sample. For genes with extreme C & G frequencies, the C & G level in the third codon position is less extreme in rat than in human. (2) Protein similarity and percentage of positive differences are the two main factors that discriminate homologous genes when characterized by differences between rat and human. By definition, positive differences result from silent changes between A or T and C or G with a direction implying a C & G content variation in the same direction as the overall gene variation. (3) For genes showing both codon usage change and low protein similarity, a majority of amino acid replacements contributes to C & G level variation in positions I and II in the same direction as the variation in position III. This is thus a new example of protein evolution due to constraints acting at the DNA level. (4) In heavy isochores (high C & G content) no direct correlation exists between codon usage change (measured by the dissymmetry of differences) and silent dissimilarity. In light isochores the opposite situation is observed: modification of codon usage is associated with a high synonymous dissimilarity. This result shows that, in some cases, modification of constrains acting at the DNA level could accelerate divergence between genomes.

Mode of assembly of amphipathic helical segments in model high-density lipoproteins

The structure of discoidal apo A-I-phospholipid complexes, representing the metabolic precursors of mature high-density lipoprotein particles, was studied by a combination of both a theoretical and an experimental approach. The secondary structure of the complex was determined by circular dichroic measurements, while the relative orientation of the apo A-I helical segments and of the phospholipid acyl chains was determined by ATR infrared measurements. Fluorescence energy transfer between the tryptophan residues of apo A-I and fluorescent phospholipid probes yielded an estimation of the relative topography of the lipid and apolipoprotein components in discoidal and spherical particles. The theoretical approach consisted of the identification of the helical segments in various apo A-I species. These segments were then oriented at a lipid/water interface by minimization of their hydrophobic and hydrophilic transfer energies. The calculation of the hydrophobicity profiles along the axis of the helices leads to the identification of specific interactions between pairs of helices. The helices were further assembled together with the phospholipids by computer modelling, enabling an estimation of the dimensions of the complex. The combination of the experimental and theoretical results yielded a model for discoidal apolipoprotein-phospholipid complexes, in which the amphipathic helical segments are oriented along the edges of the discs. Such a model can be extended to the conversion of these complexes into mature spherical HDL, through the formation of a cholesteryl ester core.

A repeating amino acid motif in CDC23 defines a family of proteins and a new relationship among genes required for mitosis and RNA synthesis

We have identified and characterized a novel, repeating 34 amino acid motif (the TPR motif) that is reiterated several times within the CDC23 gene product of S. cerevisiae. Multiple copies of this motif were discovered in five other proteins, three encoded by cell division cycle genes required to complete mitosis and two involved in RNA synthesis. Quantitative sequence analyses suggest the existence of a common underlying structure in each TPR unit that consists of amphipathic alpha-helical regions punctuated by proline-induced turns. The TPR motif defines a new family of genes and an important structural unit common to several proteins whose functions are required for mitosis and RNA synthesis.

Role of amphipathic helixes in HDL structure/function

In a recent analysis we classified amphipathic helix domains into a minimum of seven distinct classes. Four amphipathic helix classes are found in lipid-associating proteins: apolipoproteins, certain polypeptide hormones, polypeptide venoms and antibiotics, and certain complex transmembrane proteins. Three amphipathic helix classes are involved in both intra- and intermolecular protein-protein interactions: calmodulin-regulated protein kinases, coiled-coil containing proteins that include the so-called leucine zipper, and globular helical proteins. Three central hypothesis have been developed in our studies of the apolipoprotein class of amphipathic helixes: 1) The "Snorkel" hypothesis proposes that when the amphipathic helix is associated with phospholipid, amphipathic basic residues extend toward the polar face of the helix to insert their charged residues into the aqueous milieu: thus the entirety of the uncharged van der Waals' surface of the amphipathic helix is buried within the lipid. 2) We have formulated a hypothesis that Glutamyl residues located at positions 78 and 111 in apolipoprotein A-I on the nonpolar face of two amphipathic helical domains are critical to LCAT activation. 3) The hinged-domain hypothesis was proposed to explain the structural basis for the quantization of HDL subspecies, protein-protein interactions in HDL, and the HDL disc to sphere transformation.

Comparative molecular properties of swine and human very low density lipoproteins-apoproteins E and C

1. By means of 2-dimensional gradient-gel electrophoresis, the very low density lipoproteins (VLDL) apoproteins E and C profiles from human and swine plasma were studied. 2. The molecular properties (isoelectric point and molecular weight) of the VLDL apoproteins and their isoforms were determined and showed many similarities between species. 3. It also appears evident that a previously unrecognized apoprotein (C-III) and several associated isoforms may exist in swine; however, it's mobility on 2-dimensional gradient gels is very similar to Apo C-II.

Use of synthetic peptide analogues to localize lecithin:cholesterol acyltransferase activating domain in apolipoprotein A-I

The major protein of high density lipoprotein (HDL), apolipoprotein (apo) A-I, is the major activator of the plasma enzyme lecithin:cholesterol acyltransferase (LCAT). A consensus amino acid sequence has been defined for the eight, 22-residue long, tandem amphipathic helical repeats located in the carboxy-terminal region of apo A-I. A series of 22 and 44mer synthetic peptide analogues of the consensus domain, differing only in their 13th amino acid residue, were prepared and tested for LCAT activation. One of the peptides was found to equal apo A-I in LCAT activation. This is the first time a peptide activator for LCAT that rivals the activity of apo A-I in the vesicular and discoidal egg phosphatidylcholine assay systems has been synthesized. Based on these results, we propose that the major LCAT-activating domain of apo A-I resides in the 22mer tandem repeats, each containing Glu at the 13th residue and located between residues 66 and 121 in the native apolipoprotein.

The hyperlipoproteinemias

The association of disturbances of plasma lipid transport and atherogenesis has been recognized, and scientific data continue to accumulate to explain this association from a mechanistic viewpoint. A number of recent clinical trials have shown that cholesterol-lowering therapy can prevent the complications of atherosclerosis. Consequently, the attention of physicians to therapeutic intervention has increased and public awareness to plasma cholesterol levels has been heightened. This article summarizes current knowledge of how plasma lipid transport is regulated. The classical primary hyperlipoproteinemias are considered and hyperlipoproteinemias occurring secondary to other diseases are discussed. Standard methods to diagnose the defined genetic hyperlipidemias are outlined, and new approaches to assess risk of atherosclerosis are examined. Finally, the role of dietary measures and drugs in lowering blood lipids and reducing risk of coronary heart disease is delineated.

Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes

Based on the rates of synonymous substitution in 42 protein-coding gene pairs from rat and human, a correlation is shown to exist between the frequency of the nucleotides in all positions of the codon and the synonymous substitution rate. The correlation coefficients were positive for A and T and negative for C and G. This means that AT-rich genes accumulate more synonymous substitutions than GC-rich genes. Biased patterns of mutation could not account for this phenomenon. Thus, the variation in synonymous substitution rates and the resulting unequal codon usage must be the consequence of selection against A and T in synonymous positions. Most of the variation in rates of synonymous substitution can be explained by the nucleotide composition in synonymous positions. Codon-anticodon interactions, dinucleotide frequencies, and contextual factors influence neither the rates of synonymous substitution nor codon usage. Interestingly, the nucleotide in the second position of codons (always a nonsynonymous position) was found to affect the rate of synonymous substitution. This finding links the rate of nonsynonymous substitution with the synonymous rate. Consequently, highly conservative proteins are expected to be encoded by genes that evolve slowly in terms of synonymous substitutions, and are consequently highly biased in their codon usage.

The apolipoprotein multigene family: structure, expression, evolution, and molecular genetics

The plasma apolipoproteins can be classified into two subgroups: the soluble apolipoproteins including apolipoprotein (apo) A-I, A-II, A-IV, C-I, C-II, C-III, and E, and the apoBs including apoB-100 and apoB-48. The soluble apolipoproteins have very similar genomic structures, each having a total of three introns at the same locations; apoA-IV is an exception in that it has lost its first intron. Using the exon/intron junctions as reference points, we can obtain an alignment of the coding regions of all the soluble apolipoprotein genes. The mature peptide regions of the genes are almost completely made up of tandem repeats of 11 codons. The part of mature peptide region encoded by exon 3 contains a common block of 33 codons, whereas the part encoded by exon 4 contains a much more variable number of internal repeats of 11 codons. On the basis of the degree of homology of the various sequences, and the pattern of the internal repeats in these genes, an evolutionary tree has been proposed for the soluble apolipoprotein genes. ApoB-100 differs considerably from the soluble apolipoproteins. It is the largest apolipoprotein containing 4536 amino acid residues. Two types of internal repeats are identified in apoB-100: amphipathic alpha-helical repeats and proline-containing repeats with high beta-sheet content. The apoB gene contains 29 exons and 28 introns. Its evolutionary relationship to the soluble apolipoprotein genes is unclear. The 3' end of the apoB gene contains a region of variable number of tandem 12-16-base pair repeats.(ABSTRACT TRUNCATED AT 250 WORDS)

Synthesis, modification, and flotation properties of rat hepatocyte apolipoproteins

We have studied apolipoprotein synthesis, intracellular modification and secretion by primary adult rat hepatocyte cultures using continuous pulse or pulse chase labeling with [35S]methionine, immunoprecipitation and two-dimensional isoelectric focusing/polyacrylamide gel electrophoresis. The flotation properties of the newly secreted apolipoproteins were studied by discontinuous density gradient ultracentrifugation and one- and two-dimensional polyacrylamide gel electrophoresis. These studies showed that rat hepatocyte apoE is modified intracellularly to produce minor isoproteins that differ in size and charge. One of these minor isoproteins represents a monosialated apoE form (apoE3s1). Similarly, apoCIII is modified intracellularly to produce a disialated apoCIII form (apoCIIIs2), whereas newly synthesized apoA-I and apoA-IV are not glycosylated and overlap on two-dimensional gels with the proapoA-I and the plasma apoA-IV form, respectively. Both unmodified and modified apolipoproteins are secreted into the medium. Separation of secreted apolipoproteins by density gradient ultracentrifugation has shown that 50% of apoE, 80% of apoA-I, and more than 90% of apoA-IV and apoCIII are secreted in a lipid-poor form, whereas apoB-100 and apoB-48 are 100% associated with lipids. ApoB-100 floats in the VLDL and IDL regions, whereas apoB-48 is found in all lipoprotein fractions. ApoE and small amounts of apoA-I, apoA-IV and apoCIII float in the HDL region. Small amounts of apoE and apoCIII are also found in the VLDL and IDL regions, and apoE in the LDL region. Ultracentrifugation of nascent lipoproteins in the presence of rat serum promoted flotation of apoA-I and apoA-IV in the HDL fraction and resulted in increased flotation and distribution of apoE and apoCs in VLDL, IDL and LDL regions. These observations are consistent with the hypothesis that intracellular assembly of lipoproteins involves apoB-48 and apoB-100 forms, whereas a large portion of apoA-I, apoCIII and apoA-IV can be secreted in a lipid-poor form, which associates extracellularly with preexisting lipoproteins.

The baboon gene for apolipoprotein A-I: characterization of a cDNA clone and identification of DNA polymorphisms for genetic studies of cholesterol metabolism

We have isolated and sequenced a baboon apolipoprotein A-I (ApoA-I) clone from a liver cDNA library using a human cDNA hybridization probe. This baboon cDNA contains the entire ApoA-I coding region (801 bp, 267 aa), a 3' untranslated region, and a poly(A)tail. Among comparisons with apoAI sequences from other species, the baboon cDNA is most similar to that of the cynomolgus macaque (99.2% homologous) and least similar to the rat sequence (72.6% homologous). A high frequency of nonsynonymous substitutions are observed by alignment of baboon and human apoAI cDNAs, but comparisons of hydrophilicity profiles show that protein structure is conserved by substitutions of aa with similar properties. A polymorphic PstI cleavage site was identified by Southern blot analysis and subsequently mapped to the 5' end of the baboon apoAI gene. To identify effects of apoAI allelic variation on cholesterol metabolism, we used immunoblotting to compare the distributions of ApoA-I among lipoprotein size classes in baboons from each genotype under basal and atherogenic diets. We observed an increase of ApoA-I in high density lipoprotein (size class 1) particles after atherogenic diets in homozygotes for one allele, as compared to slight decreases in the other genotypes.

Proposed folding pattern for apolipoprotein A-II based on a structural analogy with uteroglobin

The tertiary structure observed in the crystalline state for uteroglobin, a small steroid binding protein, is used as a template to build an approximated model for apolipoprotein A-II. The presence of four proline residues and four hydrophobic clusters located at similar positions in apolipoprotein A-II and uteroglobin is taken as the major source of stability in such tertiary structures. A brief description of plausible specific binding sites appearing on the model of apolipoprotein A-II is given. It is suggested that the internal cavity and the four surface pockets observed for uteroglobin and postulated for apolipoprotein A-II might be used to insure specific binding of triglycerides, phospholipids, or cholesterol.

Regional chromosomal localisation of APOA2 to 1q21-1q23

Using in situ hybridisation, we have mapped APOA2 to the 1q21-1q23 region of chromosome 1. DNA hybridisation to somatic cell hybrids made from cells carrying a balanced translocation between X and 1 confirms the localisation as proximal to 1q23. This was further confirmed by the presence of two polymorphic alleles in a cell line carrying a deletion of 1q25-1q32.

Different cis-acting DNA elements control expression of the human apolipoprotein AI gene in different cell types

In mammals, the gene coding for apolipoprotein AI (apoAI), a protein of the plasma lipid transport system, is expressed only in the liver and the intestine. A series of plasmids containing various lengths of sequences flanking the 5' end of the human apoAI gene were constructed and assayed for transient expression after introduction into cultured human hepatoma (HepG2), colon carcinoma (Caco-2), and epithelial (HeLa) cells. The results showed that while most of these constructs are expressed in HepG2 and Caco-2 cells, none of them is expressed in HeLa cells. In addition, the results indicated that a DNA segment located between nucleotides -256 and -41 upstream from the transcription start site of this gene is necessary and sufficient for maximal levels of expression in HepG2 but not in Caco-2 cells, while a DNA segment located between nucleotides -2052 and -192 is required for maximal levels of expression in Caco-2 cells. Moreover, it was shown that the -256 to -41 DNA segment functions as a hepatoma cell-specific transcriptional enhancer with both homologous and heterologous promoters. These results indicate that different cis- and possibly trans-acting factors are involved in the establishment and subsequent regulation of expression of the apoAI gene in the mammalian liver and intestine.

The baboon apolipoprotein E gene: structure, expression, and linkage with the gene for apolipoprotein C-1

To develop the baboon model for molecular genetic studies of atherosclerosis, we have cloned and sequenced the baboon apolipoprotein E (apo E) gene. The baboon apo E gene encodes the E4 isoform with respect to specific amino acid positions, suggesting that the common epsilon 3 allele is not the primal human allele. Rather than accumulating predominantly synonymous nucleotide changes, 50% of substitutions in human and baboon apo E gene coding regions cause amino acid substitutions. However, comparisons of these apo E proteins show conservation of amphipathic helices required for apo E--lipid interactions. The human and baboon apo E genes have diverged less extensively than those from rat and mouse, providing further evidence for a slowing of molecular evolution in primate species. The baboon and rhesus monkey apo E genes (intron 2) contain two Alu repeats that are absent in the human gene, indicating insertion after the divergence of human and cercopithecine lineages, but before the baboon/rhesus divergence. S1 nuclease studies show that transcription of the baboon apo E gene starts at two different positions, one of which corresponds to the human gene start site. To examine linkage of apolipoprotein genes in the baboon genome, we have used a human cDNA probe to detect apo C-I gene sequences approximately 4 kb from the 3' end of the baboon apo E gene.

Time for acquiring a new gene by duplication

In view of the widespread occurrence of gene families in eukaryotic genomes that suggests the importance of gene duplication in evolution, a population genetic model incorporating unequal crossing-over was formulated. By using this model, the time needed for acquiring a new gene is investigated by an approximate analytical method and by computer simulations. The model assumes that natural selection favors those chromosomes with more beneficial genes than other chromosomes in the population, as well as random genetic drift, mutation, and unequal crossing-over. Starting from a single gene copy, it is found that the time for acquiring another gene with a new function is dependent on the rates of occurrence of unequal crossing-over and mutation. Within a realistic range of parameter values, the required time was at least several times 4N generations, where N is the effective population size. Interchromosomal unequal crossing-over at meiosis is more effective than intrachromosomal (between sister chromatids) unequal crossing-over for obtaining a new gene, provided that other parameters are the same. However, the genetic load for acquiring a gene is larger under the model of interchromosomal crossing-over. The relevance of this finding to the advantage of sexual reproduction is discussed.

A physical map of the apolipoprotein gene cluster on human chromosome 19

We have generated a restriction map around the cloned genes for human apolipoproteins CI, CII, and E by pulsed-field gel analysis. We show that the genes are clustered within an area of about 50 kb on chromosome 19. The genes are all oriented in the same direction, head to tail.

Different cis-acting DNA elements control expression of the human apolipoprotein AI gene in different cell types

In mammals, the gene coding for apolipoprotein AI (apoAI), a protein of the plasma lipid transport system, is expressed only in the liver and the intestine. A series of plasmids containing various lengths of sequences flanking the 5' end of the human apoAI gene were constructed and assayed for transient expression after introduction into cultured human hepatoma (HepG2), colon carcinoma (Caco-2), and epithelial (HeLa) cells. The results showed that while most of these constructs are expressed in HepG2 and Caco-2 cells, none of them is expressed in HeLa cells. In addition, the results indicated that a DNA segment located between nucleotides -256 and -41 upstream from the transcription start site of this gene is necessary and sufficient for maximal levels of expression in HepG2 but not in Caco-2 cells, while a DNA segment located between nucleotides -2052 and -192 is required for maximal levels of expression in Caco-2 cells. Moreover, it was shown that the -256 to -41 DNA segment functions as a hepatoma cell-specific transcriptional enhancer with both homologous and heterologous promoters. These results indicate that different cis- and possibly trans-acting factors are involved in the establishment and subsequent regulation of expression of the apoAI gene in the mammalian liver and intestine.

Apolipoprotein E polymorphism and atherosclerosis

The apo E locus contributes to determining the variation in plasma cholesterol levels of healthy and diseased populations. It also influences the expression of hyperlipidemia and appears to modulate the susceptibility to atherosclerosis in a complex multifactorial interaction. There is evidence that the presence of apo E2 is protective, whereas that of apo E4 predisposes to coronary artery disease. The burden of proof, however, lies on future, well-designed clinical trials and prospective studies. The study of the biological significance of the apo E polymorphism in humans has emphasized the importance of gene-gene and gene-environment interactions in the pathogenesis of hyperlipidemia and atherosclerosis. The apo E polymorphism involves the coding region of the apo E gene and results in alterations of the gene product which, in turn, either directly or secondarily affect the metabolic fate of the lipoprotein particles. Rapid advances in knowledge over the last decade have provided a metabolic explanation for the observation of the opposite effects of the epsilon 4 and the epsilon 2 alleles on lipoprotein levels. Apo E2 has lower receptor binding affinity which results in delayed clearance of apo E2-bearing lipoprotein particles from plasma. Apo E4 is distributed differently from apo E3 between VLDL and HDL, is degraded more rapidly than apo E3, and may enhance the catabolism of E4-bearing particles, leading to other alterations in lipoprotein metabolism which result in elevated levels of LDL. In view of the significant opposite impacts of the epsilon 4 and the epsilon 2 alleles on plasma LDL cholesterol concentrations, it is evident that determination of the apo E phenotype will become a useful adjunct to the assessment of the cardiovascular risk profile of an individual. In addition, the relationship between the epsilon 2 allele and type III hyperlipoproteinemia provides a valuable model for the study of complex genetic interactions in the pathogenesis of hyperlipidemia. The further study of apo E and its interactions shows great promise for a deeper comprehension of the pathogenesis of atherosclerosis.

Apolipoprotein gene cluster on chromosome 19. Definite localization of the APOC2 gene and the polymorphic Hpa I site associated with type III hyperlipoproteinemia

Recently, using an APOE cDNA probe, we discovered an Hpa I restriction fragment length polymorphism (RFLP) that appeared to be strongly associated with the expression of type III hyperlipoproteinemia (Klasen et al. 1987). In the present report it is shown that the same Hpa I RFLP can be revealed with both the APOC1 and APOC2 cDNA probes. This enabled us to localize the polymorphic Hpa I site between the APOE and APOC1 genes and to localize the APOC2 gene approximately 22 kb 3' of the APOC1 pseudogene on chromosome 19.

Detecting homology of distantly related proteins with consensus sequences

A simple protocol is described that is suitable for the detection of distantly related members of a protein family. In this procedure, similarity to a consensus sequence is used to distinguish chance similarity from similarity due to common ancestry. The consensus sequence is constructed from the sequences of established members of a protein family and it incorporates features characteristic of the protein fold of this family: conserved residues, the pattern of variable and conserved segments, preferred location of gaps etc. The database is searched with the consensus sequence, using the unitary matrix or log odds matrix for scoring the alignments, with variable gap penalty. The advantage of the method is that it weights key residues, ignores sequence similarity in variable segments (thus partially eliminating "background noise" coming from chance similarity), distinguishes gaps disrupting conserved segments from those occurring in positions known to be tolerant of gap events. The utility of the method was demonstrated in the case of the protein family homologous with the internal repeats of complement B as well as the internal repeats identified in fibroblast proteoglycan PG40. The consensus sequence method succeeded in finding some new members of these protein families that could not be detected by earlier methods of sequence comparison.

Changing patterns of transcriptional and post-transcriptional control of liver-specific gene expression during rat development

Genes coding for unique or tissue-specific (differentiated) functions in the liver are induced at different times during development. It has generally been felt that transcriptional control represents the dominant mechanism for regulating expression of these genes. We have determined the relative transcription rates and mRNA steady-state levels for a series of genes specifically or preferentially expressed in rat liver and find examples of transcriptional control (albumin, alpha-fetoprotein, alpha 1-antitrypsin, tyrosine aminotransferase, transferrin, and cytochrome P450, TF-1) and post-transcriptional control (alpha 1-acid glycoprotein, apolipoproteins A-1 and E, malic enzyme, and ATP citrate lyase), as well as "mixed" regulation (ligandin and cytochrome P450, R17). Examples have been identified in which the predominant mode for regulating expression of preferentially expressed genes changes from transcriptional to post-transcriptional at different stages of liver development and some members of multigene families (cytochrome P450s and apolipoprotein genes) also show independent and sometimes contrasting modes of regulation. Therefore, it appears that regulation of specific gene expression in the liver is a dynamic process, far more complex than heretofore suspected, and a much greater contribution of post-transcriptional regulation accounts for changes in expression of genes representing major functions of the liver.

Chicken apolipoprotein A-I: cDNA sequence, tissue expression and evolution

Using an antibody against chicken apolipoprotein (apo) A-I, we identified multiple cDNA clones for the protein in two intestinal cDNA libraries in lambda gt11. The complete nucleotide sequence of chicken apoA-I cDNA was determined. The sequence predicts a mature protein of 240 amino acids, a 6-amino acid propeptide and an 18-amino acid signal peptide. Using a 32P-cDNA probe, we detected the presence of apoA-I mRNA in 21 day old chicken intestine, liver, kidney, spleen, breast muscle and brain. The primary sequence of apoA-I contains numerous tandem repeats of 11 and 22 residues in a manner similar to the mammalian proteins. Our analysis of apoA-I sequences from human, rabbit, dog, rat, and chicken indicates that the rate of amino acid substitution is considerably faster in the rat lineage than in other mammalian lineages.

Precursor-product relationship between vitellogenin and the yolk proteins as derived from the complete sequence of a Xenopus vitellogenin gene

In Xenopus laevis four estrogen-responsive genes are expressed simultaneously to produce vitellogenin, the precursor of the yolk proteins. One of these four genes, the gene A2, was sequenced completely, as well as cDNAs representing 75% of the coding region of the gene. From this data the exon-intron structure of the gene was established, revealing 35 exons that give a transcript of 5,619 bp without the poly A-tail. This A2 transcript encodes a vitellogenin of 1,807 amino acids, whose structure is discussed with respect to its function. At the nucleic acid as well as at the protein level no extensive homologies with any sequences other than vitellogenin were observed. Comparison of the amino acid sequence of the vitellogenin A2 molecule with biochemical data obtained from the different yolk proteins allowed us to localize the cleavage products on the vitellogenin precursor as follows: NH2 - lipovitellin I - phosvitin (or phosvette II - phosvette I) - lipovitellin II - COOH.

Ubiquitin genes as a paradigm of concerted evolution of tandem repeats

Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken, Xenopus, Drosophila, barley, and yeast have recently been determined. By analysis of these data we show that ubiquitin is evolving more slowly than any other known protein, and that this (together with its gene organization) contributes to an ideal situation for the occurrence of concerted evolution of tandem repeats. By contrast, there is little evidence of between-cluster concerted evolution. We deduce that in ubiquitin genes, concerted evolution involves both unequal crossover and gene conversion, and that the average time since two repeated units within the polyubiquitin locus most recently shared a common ancestor is approximately 38 million years (Myr) in mammals, but perhaps only 11 Myr in Drosophila. The extreme conservatism of ubiquitin evolution also allows the inference that certain synonymous serine codons differing at the first two positions were probably mutated at single steps.