Molecular evolution of myoglobin and the fossil record: a phylogenetic synthesis

Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers

The speciose mammalian order Eulipotyphla (moles, shrews, hedgehogs, solenodons) combines an unusual diversity of semi-aquatic, semi-fossorial, and fossorial forms that arose from terrestrial forbearers. However, our understanding of the ecomorphological pathways leading to these lifestyles has been confounded by a fragmentary fossil record, unresolved phylogenetic relationships, and potential morphological convergence, calling for novel approaches. The net surface charge of the oxygen-storing muscle protein myoglobin (ZMb), which can be readily determined from its primary structure, provides an objective target to address this question due to mechanistic linkages with myoglobin concentration. Here, we generate a comprehensive 71 species molecular phylogeny that resolves previously intractable intra-family relationships and then ancestrally reconstruct ZMb evolution to identify ancient lifestyle transitions based on protein sequence alone. Our phylogenetically informed analyses confidently resolve fossorial habits having evolved twice in talpid moles and reveal five independent secondary aquatic transitions in the order housing the world's smallest endothermic divers.

Genomic expansion across the albumin gene family on human chromosome 4q is directional

The albumin gene family arose in a series of duplication events which gave rise to symmetry in its structure. The four genes are tandemly linked on human chromosome 4q in the order: 5'ALB-5'AFP-5'ALF-5'DBP-centromere, and their introns display a symmetrical and repetitive pattern that is shared by members of the gene family. These repetitive motifs provide an internal reference, allowing observations of evolutionary changes within a single line (human) of evolutionary descent. The four genes and three intergenic regions between them increase in size as they get closer to the centromere. An invasion by multiple repetitive DNA elements may account, in part, for this expansion.

Sequence characteristics of a cervid DNA repeat family

The (G + C) distribution and the presence and amounts of repetitive sequence families in the white-tailed deer (Odocoileus virginianus) have been examined. The distribution ranges from 20 to 70% (G+C) and shows four distinct repeat families. A 0.7-kb family, DII, corresponds to satellite II in domestic bovids--ox, sheep, and goat--and was singled out for detailed characterization. DII has a prototypic repeat of 67% (G + C), consists of 25,000 tandem copies, and contributes 1.7% to the genomic DNA. Sequencing and electrophoretic analysis indicate a repeat length of 691 bp. These characteristics are similar to those of the bovid satellite II families as well as to those of other cervids that we have examined. The intraspecific sequence divergence within this family has a variance of only 2.5 +/- 0.3%.

Amino-acid sequence of a cooperative, dimeric myoglobin from the gastropod mollusc, Buccinum undatum L

The complete amino-acid sequence of a dimeric myoglobin from the radular mussel of the gastropod mollusc, Buccinum undatum L. has been determined. The globin, which shows cooperative binding of oxygen, contains 146 amino acids, is N-terminal aminoacetylated, and has histidine residues at position 65 and 97, corresponding to the heme-binding histidines seen in mammalian myoglobins. It shows about 75% and 50% homology, respectively, with the dimeric molluscan myoglobins from Busycon canaliculatum and Cerithidea rhizophorarum, the former of which also shows weak cooperatively, but much less similarity to other species of myoglobin and hemoglobin.

Molecular evolution: codes, clocks, genes and genomes

The discoveries, advancements and continuing controversies in the field of molecular evolution are reviewed. Topics summarized are (1) the evolution of the genetic code, (2) gene evolution including the demonstration of homology, estimation of sequence divergence, phylogenetic trees, the molecular clock and the origin of genes and gene families by various genetic mechanisms, and (3) eukaryotic genome evolution, including the highly repeated satellite sequences, the interspersed and potentially mobile repeated sequences and the unique sequence fraction of the genome.

Genetic variants of ribosomal DNA and mitochondrial DNA between swamp and river buffaloes

To clarify the genetic relationship between Swamp and River buffaloes, the restriction fragment length polymorphisms (RFLPs) of nuclear genomic ribosomal DNA (rDNA) and cytoplasmic mitochondrial DNA (mtDNA) were analysed. Blood or liver samples from 73 Swamp and three River buffaloes were collected in East and South-east Asian countries. DNA samples from cattle, goats and sheep were used for comparisons. The analysis of rDNA allowed water buffaloes, cattle, goats and sheep to be characterized by four distinct repeat-types. However, swamp and river buffaloes showed the same repeat-type. Divergence of water buffalo and cattle is considered to have occurred approximately four to six million years ago. The RFLPs for mtDNA divided water buffaloes into three haplotypes, swamp-1, swamp-2 and river types. Swamp-1 accounted for 91% of all swamp buffaloes while swamp-2 was observed only in water buffaloes from Thailand (9%). All river buffaloes were of the same haplotype. No differences were observed between swamp and river buffaloes at the rDNA level. In contrast, a few distinct differences between them were found at the mtDNA level. Therefore, mtDNA polymorphisms provide an adequate means for classifying water buffaloes into either swamp or river buffaloes.

The primary structure of piscine (Oncorhynchus mykiss) retinol-binding protein and a comparison with the three-dimensional structure of mammalian retinol-binding protein

1. The primary structures of two variants of rainbow trout (Oncorhynchus mykiss) plasma retinol-binding protein (RBP) were determined and found to be approximately 60% identical with those of both human and Xenopus laevis RBPs. The comparable sequence similarities that we have found agree with the estimate of similar divergence times between bony fishes and mammals and between bony fishes and amphibians. The two piscine RBP variants differ by six amino acid substitutions at positions that are not crucial for the interaction with retinol, on the basis of the human RBP three-dimensional structure [Cowan, S. W., Newcomer, M. E. & Jones, T. A. (1990) Proteins Struct. Func. Genet. 8, 44-61]. 2. Models were developed for the three-dimensional structures of rainbow trout and X. laevis RBPs, based on that of human RBP. The overall three-dimensional structure appears to be very well preserved for RBPs isolated from vertebrate species for which the divergence time is 350-400 million years. At variance with an almost absolute conservation for the residues that participate in the formation of the retinol binding site in mammalian RBPs, several amino acid replacements are found for this part of the RBP molecule when the comparison is extended to piscine and amphibian RBPs. However, the only allowed amino acid replacements are either conservative or more than 0.4 nm distant from retinol. Besides the retinol binding site, a few regions at the protein surface appear to be rather conserved during phylogenetic development of vertebrates and, therefore, might be involved in molecular interactions.

Genomic organisation and sequence of the extracellular domain exons of the bovine Fc gamma RI receptor, and evidence for restricted binding of ruminant IgG to U937 cells

Southern blotting of bovine genomic DNA and hybridization with a human Fc gamma RI cDNA probe, p135, has identified a single copy of the bovine Fc gamma RI gene. A bovine genomic lymphocyte library in lambda EMBL3 was screened with probe p135. A positive lambda clone, 15.5.4, containing the three extracellular domain exons of Fc gamma RI, has been cloned, mapped and sequenced. Each extracellular domain is encoded within a single exon. All three domains are assigned to the C-2 set of the Ig superfamily with 58% identity between amino acid residues of bovine, human and mouse Fc gamma RI. Pairs of cysteine residues are conserved in each domain as potential sites for intra-chain disulphide bonding. Human monocytoid U937 cells were used as a model to test binding homology within the Fc gamma RI family. The binding of IgG isotypes to IFN-gamma stimulated U937 cells was determined by FACScan flow cytometry. U937 cell Fc gamma RI receptor does not bind bovine or ovine IgG isotypes. On the basis of these studies and by comparison of the Fc determinant region sequences of IgG, the introduction of species specificity in Fc gamma RI/IgG interaction by evolutionary drift is proposed.

Sequence and comparative analysis of the rabbit alpha-like globin gene cluster reveals a rapid mode of evolution in a G + C-rich region of mammalian genomes

A sequence of 10,621 base-pairs from the alpha-like globin gene cluster of rabbit has been determined. It includes the sequence of gene zeta 1 (a pseudogene for the rabbit embryonic zeta-globin), the functional rabbit alpha-globin gene, and the theta 1 pseudogene, along with the sequences of eight C repeats (short interspersed repeats in rabbit) and a J sequence implicated in recombination. The region is quite G + C-rich (62%) and contains two CpG islands. As expected for a very G + C-rich region, it has an abundance of open reading frames, but few of the long open reading frames are associated with the coding regions of genes. Alignments between the sequences of the rabbit and human alpha-like globin gene clusters reveal matches primarily in the immediate vicinity of genes and CpG islands, while the intergenic regions of these gene clusters have many fewer matches than are seen between the beta-like globin gene clusters of these two species. Furthermore, the non-coding sequences in this portion of the rabbit alpha-like globin gene cluster are shorter than in human, indicating a strong tendency either for sequence contraction in the rabbit gene cluster or for expansion in the human gene cluster. Thus, the intergenic regions of the alpha-like globin gene clusters have evolved in a relatively fast mode since the mammalian radiation, but not exclusively by nucleotide substitution. Despite this rapid mode of evolution, some strong matches are found 5' to the start sites of the human and rabbit alpha genes, perhaps indicating conservation of a regulatory element. The rabbit J sequence is over 1000 base-pairs long; it contains a C repeat at its 5' end and an internal region of homology to the 3'-untranslated region of the alpha-globin gene. Part of the rabbit J sequence matches with sequences within the X homology block in human. Both of these regions have been implicated as hot-spots for recombination, hence the matching sequences are good candidates for such a function. All the interspersed repeats within both gene clusters are retroposon SINEs that appear to have inserted independently in the rabbit and human lineages.

Isolation, characterization, cDNA cloning and gene expression of an avian transthyretin. Implications for the evolution of structure and function of transthyretin in vertebrates

A chicken liver cDNA library was constructed in bacteriophage lambda gt10. A full-length transthyretin cDNA clone was identified by screening with rat transthyretin cDNA and was sequenced. A three-dimensional model of chicken transthyretin was obtained by computer-graphics-based prediction from the derived amino acid sequence for chicken transthyretin and from the structure of human transthyretin determined by X-ray diffraction analysis [Blake, C.C.F., Geisow, M.J., Oatley, S.J., Rérat, B. & Rérat, C. (1978) J. Mol. Biol. 121, 339-356]. The similarity of the amino acid sequences of chicken and human transthyretins was 75% overall and 100% for the central channel containing the thyroxine-binding site. Also, the organization of the transthyretin gene into exons and introns and the tissue specificity of expression of the transthyretin gene were similar in chicken and mammals, despite an evolutionary distance of about 3 x 10(8) years from their common ancestor, the Cotylosaurus. By far the highest levels of transthyretin mRNA were found in choroid plexus. The data suggest a fundamental role for the cerebral expression of transthyretin in all vertebrates. It has been proposed that this role is the transport of thyroxine from the bloodstream to the brain [Schreiber, G., Aldred, A.R., Jaworowski, A., Nilsson, C., Achen, M.G. & Segal, M.B. (1990) Am. J. Physiol. 258, R338-R345].

Essential factors determining codon usage in ubiquitin genes

Ubiquitin is ubiquitous in all eukaryotes and its amino acid sequence shows extreme conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences coding for 13 ubiquitin genes from 11 species reported so far have been compiled and analyzed. The G + C content of codon third base reveals a positive linear correlation with the genome G + C content of the corresponding species. The slope strongly suggests that the overall G + C content of codons of polyubiquitin genes clearly reflects the genome G + C content by AT/GC substitutions at the codon third position. The G + C content of ubiquitin codon third base also shows a positive linear correlation with the overall G + C content of coding regions of compiled genes, indicating the codon choices among synonymous codons reflect the average codon usage pattern of corresponding species. On the other hand, the monoubiquitin gene, which is different from the polyubiquitin gene in gene organization, gene expression, and function of the encoding protein, shows a different codon usage pattern compared with that of the polyubiquitin gene. From comparisons of the levels of synonymous substitutions among ubiquitin repeats and the homology of the amino acid sequence of the tail of monomeric ubiquitin genes, we propose that the molecular evolution of ubiquitin genes occurred as follows: Plural primitive ubiquitin sequences were dispersed on genome in ancestral eukaryotes. Some of them situated in a particular environment fused with the tail sequence to produce monomeric ubiquitin genes that were maintained across species. After divergence of species, polyubiquitin genes were formed by duplication of the other primitive ubiquitin sequences on different chromosomes. Differences in the environments in which ubiquitin genes are embedded reflect the differences in codon choice and in gene expression pattern between poly- and monomeric ubiquitin genes.

Uniformity in the nonsynonymous substitution rates of embryonic beta-globin genes of several vertebrate species

The nucleotide substitution rate in structural portions of the embryonic beta-globin genes of placental mammals is lower than that for the adult beta-globin genes. This difference occurs entirely within the class of substitutions that result in nonsynonymous (replacement) differences between these genes, and therefore represents a constraint on the structure of the mammalian embryonic beta-globin proteins relative to the adult proteins (Shapiro et al. 1983; Hardison 1984). A similar effect has also been observed in marsupial mammals (Koop and Goodman 1988). In an effort to determine whether the observed rates are evidence of a uniform degree of selective constraint on the embryonic beta-globin genes, analyses were performed that compared replacement substitution rates. The analyses reveal that embryonic beta-globin genes appear to have been fixing replacement substitutions at nearly the same average rate not only in placental and marsupial mammals but in avian and amphibian species as well. In contrast, the adult beta-globin genes from these organisms appear to have a more variable rate of replacement substitution with an especially low rate for birds. In the chicken (Gallus gallus), the adult beta-globin gene replacement substitution rate appears to be lower than the embryonic replacement substitution rate.

Identification of goat allotypic determinants and generation of goat-mouse hybridomas secreting goat IgG2

Five allotypic determinants controlled by independent genes have been identified in goat. Of these determinants, four have been detected with alloimmune antisera and one with monoclonal antibodies. The specificities A1, C1 and D1 are lipoproteins; B1 is possibly an alpha 2 macroglobulin and E1 and IgG2. The specificity B1 is not expressed until the age of 3-4 months. The gene controlling the specificity E1 is present at about the same frequency (0.38-0.41) in goat, sheep, cattle and water buffalo. Stable hybridomas secreting goat IgG2 have been obtained by the fusion of goat peripheral lymphocytes with mouse myeloma cells.

Urate oxidase: primary structure and evolutionary implications

Urate oxidase, or uricase (EC 1.7.3.3), is a peroxisomal enzyme that catalyzes the oxidation of uric acid to allantoin in most mammals. In humans and certain other primates, however, the enzyme has been lost by some unknown mechanism. To identify the molecular basis for this loss, urate oxidase cDNA clones were isolated from pig, mouse, and baboon, and their DNA sequences were determined. The mouse urate oxidase open reading frame encodes a 303-amino acid polypeptide, while the pig and baboon urate oxidase cDNAs encode a 304-amino acid polypeptide due to a single codon deletion/insertion event. The authenticity of this single additional codon was confirmed by sequencing the mouse and pig genomic copies of the gene. The urate oxidase sequence contains a domain similar to the type 2 copper binding motif found in other copper binding proteins, suggesting that the copper ion in urate oxidase is coordinated as a type 2 structure. Based upon a comparison of the NH2-terminal peptide and deduced sequences, we propose that the maturation of pig urate oxidase involves the posttranslational cleavage of a six-amino acid peptide. Two nonsense mutations were found in the human urate oxidase gene, which confirms, at the molecular level, that the urate oxidase gene in humans is nonfunctional. The sequence comparisons favor the hypothesis that the loss of urate oxidase in humans is due to a sudden mutational event rather than a progressive mutational process.

Amphibian albumins as members of the albumin, alpha-fetoprotein, vitamin D-binding protein multigene family

The Xenopus laevis 68-kd and 74-kd albumin amino acid sequences are examined with respect to their relationship to the other known members of the albumin/alpha-fetoprotein/vitamin D-binding protein gene family. Each of the three members of this family presents a unique pattern of conserved regions indicating a differential selective pressure related to specific functional characteristics. Furthermore, an evolutionary tree of these genes was deduced from the divergence times calculated from direct nucleotide sequence comparisons of individual gene pairs. These calculations indicate that the vitamin D-binding protein/albumin separation occurred 560-600 million years (Myr) ago and the albumin/alpha-fetoprotein divergence 280 Myr ago. This observation leads to the hypothesis according to which the albumin/alpha-fetoprotein gene duplication occurred shortly after the amphibian/reptile separation. Consequently, and unlike mammals, amphibians and fishes should lack an alpha-fetoprotein in their serum at larval stages, which is consistent with a recent analysis of serum proteins in Xenopus laevis larvae. This hypothesis now will have to be tested further in additional lower vertebrates.

Structure of the goat psi beta y beta-globin pseudogene. Analysis of goat pseudogene evolutionary patterns

The 12-member beta-globin gene locus of the goat contains three beta(adult)-type pseudogenes, one in each of three four-gene subsets of the locus. We have determined the complete nucleotide sequence of psi beta y, the pseudogene present in the most downstream four-gene subset, which also contains the functional fetal gene, beta F. psi beta y contains, throughout its length, numerous incapacitating mutations in common with the previously sequenced goat psi beta x and psi beta z pseudogenes consistent with the model that all were descended from a common pseudogene ancestor which became defective prior to the expansion of the beta-globin locus in the goat lineage. Evolutionary analysis of the psi beta y sequence in comparison to psi beta x and psi beta z provides evidence that nucleotide substitutions were fixed in a random manner within these pseudogenes with respect to polarity, coding versus non-coding regions, and replacement sites versus silent sites. However, substitutions appear to have accumulated asymmetrically between different pseudogenes in a manner that provides evidence for partial gene conversion. Moreover, the presence of deletions in goat psi beta y, which are also observed in the cow pseudogene psi 2, but not in the cow psi 1 pseudogene, indicate that goat psi beta y and cow psi 2 are orthologous but cow psi 1 actually arose prior to the goat/cow divergence. The authentic goat orthologue to cow psi 1 temporarily existed in the goat lineage but was deleted, probably prior to the divergence of goats and sheep.

Human glyceraldehyde-3-phosphate dehydrogenase pseudogenes: molecular evolution and a possible mechanism for amplification

We screened two human genomic libraries and isolated 14 different clones, designated lambda G1 and EG1-EG13, homologous to human glyceraldehyde-3-phosphate dehydrogenase (GAPD) cDNA. Subcloning and sequencing these recombinant phages led us to classify them as five different pseudogenes (psi G1-psi G5). All these sequences show such features typical of processed pseudogenes as numerous mutations, insertions, and deletions. The identity of numerous mutated sites among these pseudogenes and the presence of two Alu sequences flanking both ends of psi G1 suggest that GAPD pseudogenes originated from a unique reverse transcribed mRNA followed by gene duplication. The rate of nucleotide substitutions per site per year for known GAPD functional genes is low both for the synonymous substitutions (1.87 x 10(-9] and for the nonsynonymous substitutions (0.12 x 10(-9] and indicates that the GAPD cDNA sequence is well conserved not only at the amino acid level, but also at the nucleotide level. The rate of nucleotide substitutions per site per year for GAPD pseudogenes shows a higher value (5.9 x 10(-9] and suggests that these pseudogenes do not have any functional role.

Differences in the number of embryonic and pseudo-beta-globin genes between HbA and HbB sheep

DNA samples obtained from 8 goats, 1 moufflon, and 84 sheep with HbA, HbAB, and HbB belonging to different breeds were digested with BamHI, EcoRI, HindIII and PstI and probed with the 5' end of the goat epsilon IV- and psi beta Z-globin genes. Sheep homozygous for HbA show a different restriction pattern than sheep homozygous fo HbB with each of these endonucleases. The main difference is that HbB sheep lack the epsilon II and psi beta X genes. These results, in addition to those previously obtained using a probe specific for beta-globin genes, suggest that HbB sheep probably lack the preadult four-gene set. The DNAs from moufflon and sheep homozygous for HbA show indistinguishable restriction patterns. Furthermore, a number of restriction fragment length polymorphisms (RFLPs) are detected in the epsilon IV and psi beta Z DNA regions, and one HindIII RFLP in the epsilon VI DNA region.

Complete nucleotide sequence of the rabbit beta-like globin gene cluster. Analysis of intergenic sequences and comparison with the human beta-like globin gene cluster

The nucleotide sequence of the entire beta-like globin gene cluster of rabbits has been determined. This sequence of a continuous stretch of 44.5 x 10(3) base-pairs (bp) starts about 6 x 10(3) bp upstream from epsilon (the 5'-most gene) and ends about 12 x 10(3) bp downstream from beta (the 3'-most gene). Analysis of the sequence reveals that: (1) the sequence is relatively A + T rich (about 60%); (2) regions with high G + C content are associated with OcC repeats, a short interspersed repeated DNA in rabbits; (3) the distribution of polypurines, polypyrimidines and alternating purine/pyrimidine tracts is not random within the cluster; (4) most open reading frames are associated with known globin coding regions, OcC repeats or long interspersed repeats (L1 repeats); (5) the most prominent open reading frames are found in the L1 repeats; (6) different strand asymmetries in base composition are associated with embyronic and adult genes as well as the tandem L1 repeats at the 3' end of the cluster; and (7) essentially all the repeats appear to have been inserted by a transposon mechanism. A comparison of the sequence with itself by a dot-plot analysis has revealed nine new members of the OcC family of repeats in addition to the six previously reported. The OcC repeats tend to be clustered, particularly in the epsilon-gamma and gamma-psi delta intergenic regions. Dot-plot comparisons between the rabbit and the human clusters have revealed extensive sequence matches. Homology starts about 6 x 10(3) bp 5' to epsilon or as far upstream as the rabbit sequence is available. It continues throughout the entire cluster and stops about 0.7 x 10(3) bp 3' to beta, at which point several repeats have inserted in both rabbits and humans. Throughout the gene cluster, the homology is interrupted mainly by insertions or deletions in either the rabbit or the human genome. Almost all of the insertions are of known short or long repeated DNAs. The positions of the insertions are different in the two gene clusters, which indicates that both short and long repeats have been transposing throughout the genome for the time since the mammalian radiation. An alignment of rabbit and human sequences allows the calculation of the substitution rate around epsilon. Sequences far removed from the gene are evolving at a rate equivalent to the pseudogene rate, although some short regions show an apparently higher rate.(ABSTRACT TRUNCATED AT 400 WORDS)

Human cDNA clones for an alpha subunit of Gi signal-transduction protein

Two cDNA clones were obtained from a lambda gt11 cDNA human brain library that correspond to alpha i subunits of G signal-transduction proteins (where alpha i subunits refer to the alpha subunits of G proteins that inhibit adenylate cyclase). The nucleotide sequence of human brain alpha i is highly homologous to that of bovine brain alpha i [Nukada, T., Tanabe, T., Takahashi, H., Noda, M., Haga, K., Haga, T., Ichiyama, A., Kangawa, K., Hiranaga, M., Matsuo, H. & Numa, S. (1986) FEBS Lett. 197, 305-310] and the predicted amino acid sequences are identical. However, human and bovine brain alpha i cDNAs differ significantly from alpha i cDNAs from human monocytes, rat glioma, and mouse macrophages in amino acid (88% homology) and nucleotide (71-75% homology) sequences. In addition, the nucleotide sequences of the 3' untranslated regions of human and bovine brain alpha i cDNAs differ markedly from the sequences of human monocyte, rat glioma, and mouse macrophage alpha i cDNAs. These results suggest there are at least two classes of alpha i mRNA.

Analysis of a human V beta gene subfamily

We have isolated and sequenced five germline V beta gene segments that are homologous to the V region of the YT35 cDNA encoding the beta chain of the T cell antigen receptor from the tumor MOLT-3. One of these gene segments is identical to the YT35 V segment, and therefore is the corresponding germline V beta gene segment encoding the YT35 cDNA. The other four V beta members exhibit 77-98% homology to the YT35 V gene segment. Two of these V beta gene segments are pseudogenes. Analyses of the coding region sequences reveal that, although the V beta segments are very diverse, they are mutating at a rate comparable to that observed in most eukaryotic genes. Analyses of the genomic clones show that the spacing distance between germline V beta gene segments ranges from 3 kb to greater than 30 kb, and the entire V beta 8 subfamily appears to be linked by a total of no more than 110 kb of DNA.

Conserved elements in the 3' untranslated regions of c-fos and actin mRNAs

In this study, the nucleotide sequences of the 3' untranslated regions (UTR) of the mouse and human c-fos genes, and the rat and human beta-actin genes were examined. It is shown (i) that the 3' UTR of c-fos is highly conserved between mouse and man, (ii) that multiple copies of a 12 bp element occur, in clusters, in the 3' UTR both of c-fos and of beta-actin. This conserved 12 bp element is analogous to the putative repressor binding site previously identified (Renan, Bioscience Reports, 5 (1985), 739-753). These findings provide additional support for the proposal that regulatory signals are located in the 3' UTR's of certain genes.

Comparison of three actin-coding sequences in the mouse; evolutionary relationships between the actin genes of warm-blooded vertebrates

We have determined the sequences of three recombinant cDNAs complementary to different mouse actin mRNAs that contain more than 90% of the coding sequences and complete or partial 3' untranslated regions (3'UTRs): pAM 91, complementary to the actin mRNA expressed in adult skeletal muscle (alpha sk actin); pAF 81, complementary to an actin mRNA that is accumulated in fetal skeletal muscle and is the major transcript in adult cardiac muscle (alpha c actin); and pAL 41, identified as complementary to a beta nonmuscle actin mRNA on the basis of its 3'UTR sequence. As in other species, the protein sequences of these isoforms are highly (greater than 93%) conserved, but the three mRNAs show significant divergence (13.8-16.5%) at silent nucleotide positions in their coding regions. A nucleotide region located toward the 5' end shows significantly less divergence (5.6-8.7%) among the three mouse actin mRNAs; a second region, near the 3' end, also shows less divergence (6.9%), in this case between the mouse beta and alpha sk actin mRNAs. We propose that recombinational events between actin sequences may have homogenized these regions. Such events distort the calculated evolutionary distances between sequences within a species. Codon usage in the three actin mRNAs is clearly different, and indicates that there is no strict relation between the tissue type, and hence the tRNA precursor pool, and codon usage in these and other muscle mRNAs examined. Analysis of codon usage in these coding sequences in different vertebrate species indicates two tendencies: increases in bias toward the use of G and C in the third codon position in paralogous comparisons (in the order alpha c less than beta less than alpha sk), and in orthologous comparisons (in the order chicken less than rodent less than man). Comparison of actin-coding sequences between species was carried out using the Perler method of analysis. As one moves backward in time, changes at silent sites first accumulate rapidly, then begin to saturate after -(30-40) million years (MY), and actually decrease between -400 and -500 MY. Replacements or silent substitutions therefore cannot be used as evolutionary clocks for these sequences over long periods. Other phenomena, such as gene conversion or isochore compartmentalization, probably distort the estimated divergence time.

A previously undetected pseudogene in the human alpha globin gene cluster

The sequence of the DNA between two pseudogenes in the human alpha-like globin gene cluster has been determined. Comparison of this sequence with sequences from other alpha-like globin gene clusters revealed another pseudogene, psi alpha 2, between the previously recognized pseudogenes zeta 1 and psi alpha 1. Therefore, the human alpha-like globin gene family is organized 5'-zeta 2-zeta 1-psi alpha 2-psi alpha 1-alpha 2-alpha 1-3'. The new pseudogene psi alpha 2 is very close to zeta 1, beginning only 65 base pairs 3' to the polyadenylation site of zeta 1. The first exon and the first intron of psi alpha 2 are interrupted by large inserts which are flanked by short (6 to 8 base pairs) direct repeats. The pseudogene psi alpha 2 lacks a promoter for transcription by RNA polymerase II, the first exon is highly divergent, one splice site is mutated, and five different frameshift mutations have occurred in the coding regions. Thus psi alpha 2 cannot encode a globin polypeptide. This pseudogene was not recognized in previous hybridization analyses of the human alpha-like globin gene cluster, and our discovery of it by sequence analysis suggests that divergent copies of a large number of genes may comprise a substantial fraction of the slowly renaturing DNA of mammalian genomes.

Cloning and chromosomal location of the alpha- and beta-globin genes from a marsupial

The cDNA sequences encoding the adult alpha- and beta-globin polypeptides of a marsupial, the native cat Dasyurus viverrinus, have been cloned and their nucleotide sequences have been determined. Using these cDNA clones we have determined the chromosomal location of the native cat alpha- and beta-globin genes by in situ hybridization to fixed metaphase chromosomes and by hybridization to DNA extracted from chromosomes purified by a fluorescence-activated cell sorter. Using two independent methods of gene assignment we have shown the alpha- and beta-globin-like gene sequences to be asyntenic in the native cat, the alpha-globin-like sequences being on chromosome 2 and the beta-globin-like sequences being on chromosome 4.

Two distinct families of human and bovine interferon-alpha genes are coordinately expressed and encode functional polypeptides

The classical human interferon-alpha (HuIFN-alpha) gene family is estimated to consist of 15 or more nonallelic members which encode proteins sharing greater than 77% amino acid sequence homology. Low-stringency hybridization with a HuIFN-alpha cDNA probe permitted the isolation of two distinct classes of bovine IFN-alpha genes. The first subfamily (class I) is more closely related to the known HuIFN-alpha genes than to the second subfamily (class II) of bovine IFN-alpha genes. Extensive analysis of the human genome has revealed a HuIFN-alpha gene subfamily corresponding to the class II bovine IFN-alpha genes. The class I human and bovine IFN-alpha genes encode mature IFN polypeptides of 165 to 166 amino acids, whereas the class II IFN-alpha genes encode 172 amino acid proteins. Expression in Escherichia coli of members of both gene subfamilies results in polypeptides having potent antiviral activity. In contrast to previous studies which found no evidence of class II IFN-alpha protein or mRNA expression, we demonstrate that the class I and class II IFN-alpha genes are coordinately induced in response to viral infection.

Two distinct families of human and bovine interferon-alpha genes are coordinately expressed and encode functional polypeptides

The classical human interferon-alpha (HuIFN-alpha) gene family is estimated to consist of 15 or more nonallelic members which encode proteins sharing greater than 77% amino acid sequence homology. Low-stringency hybridization with a HuIFN-alpha cDNA probe permitted the isolation of two distinct classes of bovine IFN-alpha genes. The first subfamily (class I) is more closely related to the known HuIFN-alpha genes than to the second subfamily (class II) of bovine IFN-alpha genes. Extensive analysis of the human genome has revealed a HuIFN-alpha gene subfamily corresponding to the class II bovine IFN-alpha genes. The class I human and bovine IFN-alpha genes encode mature IFN polypeptides of 165 to 166 amino acids, whereas the class II IFN-alpha genes encode 172 amino acid proteins. Expression in Escherichia coli of members of both gene subfamilies results in polypeptides having potent antiviral activity. In contrast to previous studies which found no evidence of class II IFN-alpha protein or mRNA expression, we demonstrate that the class I and class II IFN-alpha genes are coordinately induced in response to viral infection.

Identification of a diversity segment of human T-cell receptor beta-chain, and comparison with the analogous murine element

The humoral immune system antigen-binding proteins (immunoglobulins) are disulphide-linked heterodimers of light and heavy chains. The gene for the variable region which determines antigen specificity is assembled when one member from each of the dispersed clusters of variable (V) gene segments, diversity (D) elements (for the heavy chains only) and joining (J) segments rearrange and fuse during B-cell development (reviewed in ref. 1). Short recognition sequences adjacent to these elements appear to be involved in the recombination process. The cellular immune system antigen recognition proteins are receptors on the surface of T cells, which are composed of disulphide-linked alpha-chains and beta-chains, each of which has a variable and constant region. Recently, cDNA clones of the beta-chain mRNA have been isolated; the genomic arrangement is very similar to immunoglobulin genes with multiple V beta genes, and two clusters of J beta segments, each of which is upstream from a constant-region gene segment. The V beta and J beta segments have adjacent recombinational recognition sequences like the immunoglobulin elements. However, approximately 10 nucleotides of the cDNA clones between the V beta and J beta regions were not present in the corresponding genomic elements and may have been due to intervening D beta segments. Here we describe a diversity element (D beta 1.1) in a region of high human-mouse homology about 650 bases 5' to the first J beta cluster. Two transcripts which include sequences upstream of D beta 1.1 are found in the human thymus. This region may have some other function besides providing the beta-chain with a diversity segment.

Structure and evolution of mammalian tRNA genes: sequence of a mouse tRNAiMet gene, the 5'-flanking region of which is homologous to a human gene

From a recombinant lambda phage, we have determined a 317-bp sequence containing a mouse tRNAiMet gene. The coding region is precisely homologous to mammalian tRNAiMet if post-transcriptional modifications (including addition of the 3'-terminal CCA) are not considered. The gene does not contain introns and has a typical RNA polymerase III termination site in the 3'-flanking region. It is transcribed by RNA polymerase III in the HeLa cell S-100 system in vitro. Notably, the 5'-flanking region of the mouse tRNAiMet gene shares a "patchwork" pattern of homology with one of the human tRNAiMet genes of Santos and Zasloff [Cell 23 (1981) 699-710]. The 5'-flanking regions of the two genes contain strings of nucleotides, 6 to 32 bp in length, the homology of which is 76-100%. These are separated by short strings of unrelated nucleotides. This is one of the first examples of tRNA genes containing homologous 5'-flanking regions isolated from distantly related mammals. We also report a novel method for constructing deletion mutants of sequences cloned in M13 vectors.

Chromosomal location of human metallothionein genes: implications for Menkes' disease

Human metallothioneins are encoded by a complex multigene family. The chromosomal location of these genes has been determined by gel transfer hybridization analysis of the DNA from human-rodent cell hybrids. Chromosome 16 contains a cluster of metallothionein sequences, including two functional metallothionein I genes and a functional metallothionein II gene. The remaining sequences, including a processed pseudogene, are dispersed to at least four other autosomes. The absence of metallothionein sequences from the X chromosome indicates that Menkes' disease, an X-linked disorder of copper metabolism, affects metallothionein expression by a trans-acting mechanism.

Ruminant globin gene structures suggest an evolutionary role for Alu-type repeats

Bovine fetal and adult globin genes were cloned and subjected to DNA sequence analysis. Both of these genes contained insertions of Alu-type repetitive DNA within their introns. Comparison of cow and goat beta-type globin genes indicates that intragenic DNA insertions played a role in their evolution. These data support the theory that Alu-type repeats maintain genetic diversity by inhibiting gene conversion.

Evolutionary conservation in the untranslated regions of actin mRNAs: DNA sequence of a human beta-actin cDNA

We report the complete nucleotide sequence of a human beta actin cDNA. Both the 5' and 3' untranslated regions of the sequence are similar (greater than 80%) to the analogous regions of the rat beta-actin gene reported by Nudel et al (1983). When a segment of the 3' untranslated region is used as a radiolabelled probe, strong hybridization to chick beta actin mRNA is seen. This conservation of sequences suggests that strong selective pressures operate on non-translated segments of beta actin mRNA.

Expression of human alpha-tubulin genes: interspecies conservation of 3' untranslated regions

To examine the sequence complexity and differential expression of human alpha-tubulin genes, we constructed cDNA libraries from two unrelated tissue types (epidermis and fetal brain). The complete sequence of a positively hybridizing alpha-tubulin clone from each library is described. Each is shown to represent an abundantly expressed gene from fetal brain and keratinocytes, respectively. Although the coding regions are extensively homologous (97%), the 3' untranslated regions are totally dissimilar. This property has been used to dissect the human alpha-tubulin multigene family into members bearing sequence relatedness in this region. Surprisingly, each of these noncoding regions shares very high (65 to 80%) interspecies homology with the 3' untranslated region of one of the two rat alpha-tubulin genes of known sequence. These unexpected homologies imply the existence of selective pressure on the 3' untranslated regions of some cytoskeletal genes which maintains sequence fidelity during the course of evolution, perhaps as a consequence of an as yet unidentified functional requirement.