A new family of tandem repetitive early histone genes in the sea urchin Lytechinus pictus: evidence for concerted evolution within tandem arrays

Concerted and birth-and-death evolution of multigene families

Until around 1990, most multigene families were thought to be subject to concerted evolution, in which all member genes of a family evolve as a unit in concert. However, phylogenetic analysis of MHC and other immune system genes showed a quite different evolutionary pattern, and a new model called birth-and-death evolution was proposed. In this model, new genes are created by gene duplication and some duplicate genes stay in the genome for a long time, whereas others are inactivated or deleted from the genome. Later investigations have shown that most non-rRNA genes including highly conserved histone or ubiquitin genes are subject to this type of evolution. However, the controversy over the two models is still continuing because the distinction between the two models becomes difficult when sequence differences are small. Unlike concerted evolution, the model of birth-and-death evolution can give some insights into the origins of new genetic systems or new phenotypic characters.

Common evolutionary origin and birth-and-death process in the replication-independent histone H1 isoforms from vertebrate and invertebrate genomes

The H1 histone multigene family shows the greatest diversity of isoforms among the five histone gene families, including replication-dependent (RD) and replication-independent (RI) genes, according to their expression patterns along the cell cycle and their genomic organization. Although the molecular characterization of the RI isoforms has been well documented in vertebrates, similar information is lacking in invertebrates. In this work we provide evidence for a polyadenylation signature in the Mytilus "orphon" H1 genes similar to the polyadenylation characteristic of RI H1 genes. These mussel genes, together with the sea urchin H1delta genes, are part of a lineage of invertebrate "orphon" H1 genes that share several control elements with vertebrate RI H1 genes. These control elements include the UCE element, H1-box and H4-box. We provide evidence for a functional evolution of vertebrate and invertebrate RI H1 genes, which exhibit a clustering pattern by type instead of by species, with a marked difference from the somatic variants. In addition, these genes display an extensive silent divergence at the nucleotide level which is always significantly larger than the nonsilent. It thus appears that RI and RD H1 isoforms display similar long-term evolutionary patterns, best described by the birth-and-death model of evolution. Notably, this observation is in contrast with the theoretical belief that clustered RD H1 genes evolve in a concerted manner. The split of the RI group from the main RD group must therefore have occurred before the divergence between vertebrates and invertebrates about 815 million years ago. This was the result of the transposition of H1 genes to solitary locations in the genome.

Cortical granule translocation is microfilament mediated and linked to meiotic maturation in the sea urchin oocyte

Cortical granules exocytose after the fusion of egg and sperm in most animals, and their contents function in the block to polyspermy by creating an impenetrable extracellular matrix. Cortical granules are synthesized throughout oogenesis and translocate en masse to the cell surface during meiosis where they remain until fertilization. As the mature oocyte is approximately 125 μm in diameter (Lytechinus variegatus), many of the cortical granules translocate upwards of 60 μm to reach the cortex within a 4 hour time window. We have investigated the mechanism of this coordinated vesicular translocation event. Although the stimulus to reinitiate meiosis in sea urchin oocytes is not known, we found many different ways to reversibly inhibit germinal vesicle breakdown, and used these findings to discover that meiotic maturation and cortical granule translocation are inseparable. We also learned that cortical granule translocation requires association with microfilaments but not microtubules. It is clear from endocytosis assays that microfilament motors are functional prior to meiosis, even though cortical granules do not use them. However, just after GVBD, cortical granules attach to microfilaments and translocate to the cell surface. This latter conclusion is based on organelle stratification within the oocyte followed by positional quantitation of the cortical granules. We conclude from these studies that maturation promoting factor (MPF) activation stimulates vesicle association with microfilaments, and is a key regulatory step in the coordinated translocation of cortical granules to the egg cortex.

Molecular evolution of the nontandemly repeated genes of the histone 3 multigene family

In some species, histone gene clusters consist of tandem arrays of each type of histone gene, whereas in other species the genes may be clustered but not arranged in tandem. In certain species, however, histone genes are found scattered across several different chromosomes. This study examines the evolution of histone 3 (H3) genes that are not arranged in large clusters of tandem repeats. Although H3 amino acid sequences are highly conserved both within and between species, we found that the nucleotide sequence divergence at synonymous sites is high, indicating that purifying selection is the major force for maintaining H3 amino acid sequence homogeneity over long-term evolution. In cases where synonymous-site divergence was low, recent gene duplication appeared to be a better explanation than gene conversion. These results, and other observations on gene inactivation, organization, and phylogeny, indicated that these H3 genes evolve according to a birth-and-death process under strong purifying selection. Thus, we found little evidence to support previous claims that all H3 proteins, regardless of their genome organization, undergo concerted evolution. Further analyses of the structure of H3 proteins revealed that the histones of higher eukaryotes might have evolved from a replication-independent-like H3 gene.

Sea urchin ovoperoxidase: oocyte-specific member of a heme-dependent peroxidase superfamily that functions in the block to polyspermy

Ovoperoxidase is one of several oocyte-specific proteins that are stored within sea urchin cortical granules, released during the cortical reaction, and incorporated into the newly formed fertilization envelope. Ovoperoxidase plays a particularly important role in this process, crosslinking the envelope into a hardened matrix that is insensitive to biochemical and mechanical challenges and thus providing a permanent block to polyspermy. Here we present the primary structures of two ovoperoxidases as predicted from cDNAs cloned from the sea urchins Strongylocentrotus purpuratus (AF035380) and Lytechinus variegatus (AF035381). We also present a proposed scheme for the post-translational processing of ovoperoxidase based upon comparisons between the cDNA and protein structures and taking into account previously published reports. The sea urchin ovoperoxidase sequences conform to a profile shared by members of a heme-dependent animal peroxidase family, including the mammalian myelo-, lacto-, eosinophil, and thyroid peroxidases. Using in situ RNA hybridizations, we showed that the mRNA of S. purpuratus ovoperoxidase (4 kb) is present exclusively in oocytes, and is turned over rapidly following germinal vesicle breakdown. Taking into account our immunoblot and N-terminal sequencing data along with reports from similar peroxidases, we propose that ovoperoxidases are synthesized in a pre-pro form and proteolytically processed to result in the 70 and 50 kDa forms that are found in the fertilization envelope. The sequence and structural data presented here will facilitate our continuing studies of the biogenesis of cortical granules and the fertilization envelope. Additionally, since ovoperoxidase activities have been reported in a wide range of animals, these cDNAs will be useful in uncovering similar peroxidases used in the fertilization reactions of other metazoan eggs.

Cortical granules of the sea urchin translocate early in oocyte maturation

Cortical granules are secretory vesicles poised at the cortex of an egg that, upon stimulation by sperm contact at fertilization, secrete their contents. These contents modify the extracellular environment and block additional sperm from reaching the egg. The role of cortical granules in blocking polyspermy is conserved throughout much of phylogeny. In the sea urchin, cortical granules accumulate throughout the cytoplasm during oogenesis, but in mature eggs the cortical granules are attached to the plasma membrane, having translocated to the cortex at some earlier time. To study the process of cortical granule translocation to the cell surface we have devised a procedure for maturation of sea urchin oocytes in vitro. Using this procedure, we examined the rate of oocyte maturation by observing the movement and breakdown of the germinal vesicle, the formation of polar bodies and the formation of the egg pronucleus. We find that oocyte maturation takes approximately 9 hours in the species used here (Lytechinus variegatus), from the earliest indication of maturation (germinal vesicle movement) to formation of a distinct pronucleus. We then observed the translocation of cortical granules in these cells by immunolocalization using a monoclonal antibody to hyalin, a protein packaged specifically in cortical granules. We found that the translocation of cortical granules in in vitro-matured oocytes begins with the movement of the germinal vesicle to the oocyte cell surface, and is 50% complete 1 hour after germinal vesicle breakdown. In the in vitro-matured egg, 99% of the cortical granules are at the cortex, indistinguishable from translocation in oocytes that mature in vivo. We have also found that eggs that mature in vitro are functionally identical to eggs that mature in vivo by four criteria. (1) The matured cells undergo a selective turnover of mRNA encoding cortical granule contents. (2) The newly formed pronucleus begins transcription of histone messages. (3) Cortical granules that translocate in vitro are capable of exocytosis upon activation by the calcium ionophore, A23187. (4) The mature egg is fertilizable and undergoes normal cleavage and development. In vitro oocyte maturation enables us to examine the mechanism of cortical granule translocation and other processes that had previously only been observed in static sections of fixed ovaries.

Avian keratin genes. II. Chromosomal arrangement and close linkage of three gene families

We describe the isolation and characterization of a set of overlapping cosmid clones that contain chicken keratin genes. The 100 kb (1 kb = 10(3) base-pairs) of DNA represented in these clones contains a cluster of 18 feather keratin genes spanning 53 kb of DNA. The feather keratin genes are spaced about 3 kb apart and at least 11 of them have the same transcriptional orientation. Southern analysis using oligonucleotide probes made from highly conserved portions of the 5' non-coding, intron and 3' non-coding regions, respectively, indicate that these sequences have been highly conserved among the gene family as a whole, with only one or two exceptions in each case. The presence of some regularly repeated restriction enzyme sites are indicative of tandem duplication events in the recent history of the feather keratin gene family. The feather keratin gene locus is flanked on both sides by related types of keratin genes. On the 5' side of the feather gene cluster are three keratin genes (designated feather-like) that are located 5 kb from the last feather keratin gene and are spaced about 4 kb apart. On the 3' side of the feather gene cluster, 21 kb from the last feather keratin gene, lies a cluster of four genes that encode claw keratins. These genes are spaced about 1 kb apart and appear to be divergently transcribed. Partial DNA sequence analysis of the feather-like gene lying proximal to the feather keratin gene cluster demonstrated that it encodes a protein of 115 amino acid residues that is 80% homologous to the feather keratins at both the DNA and amino acid sequence levels. The feather-like gene(s) are expressed in both embryonic and adult (post-hatch) chick feathers and at a very low level in embryonic scale tissue. These genes therefore form a new family of feather proteins that is distinct from the previously characterized feather keratins.

Structure of an unusual sea urchin U1 RNA gene cluster

Genomic clones containing multiple copies of the Lytechinus variegatus U1 gene have been isolated from a gene library in the phage lambda EMBL3. These clones contain both types of U1 RNA gene repeats interspersed in the same 15-kb fragment. In addition, about 1/3 of the repeat units contain a 260-bp insert 460 bp prior to the first nucleotide of the U1 RNA sequence. The inserted sequence is abundant in the sea urchin genome as judged by Southern blots of genomic DNA. There are no repeated sequences flanking the insert. The insert occurs at the same position in the highly conserved 5'-flanking region at which a deletion has previously been reported.

Structure and expression of a second sea urchin U1 RNA gene repeat

There are two tandemly repeated sets of U1 RNA genes in the sea urchin L. variegatus. Each of these genes is present in a 1.4 kb repeat defined by a HindIII site about 450 bases 5' to the gene. The sequences of a member of both repeating units (U1.1 and U1.2) has been determined. The repeats are nearly identical for 550 nucleotides 5' to the gene but show great divergence starting 30 nucleotides 3' to the gene, just after the CAAAGAAAGAAAA sequence thought to be required for 3' end formation. The other boundary between the conserved and non-conserved sequences is a polypyrimidine sequence (on the strand which codes for U1 RNA). Both of these repeats are expressed in blastula stage embryos, as judged by transcription of unique sequences 3' to the gene in nuclei isolated from blastula stage embryos. At least some of the two types of repeats are interspersed, since representatives of both repeat types on a single gamma phage isolated from a gene library. The sequence of the U1 RNA in L. variegatus eggs and embryos corresponds to the sequence of the U1 repeat.

Complete sequence of three alpha-tubulin cDNAs in Chinese hamster ovary cells: each encodes a distinct alpha-tubulin isoprotein

The genome of Chinese hamster ovary (CHO) cells contains a complex family of approximately 16 alpha-tubulin genes, many of which may be pseudogenes. We present here the complete cDNA sequences of three expressed alpha-tubulin genes; one of these genes has been identified only in CHO cells. The noncoding regions of these three CHO alpha-tubulin genes differed significantly, but their coding regions were highly conserved. Nevertheless, we observed differences in the predicted amino acid sequences for the three genes. A comparison of the CHO alpha-tubulin sequences with all of the sequences available for mammals allowed assignment of the alpha-tubulin genes to three classes. The proteins encoded by the members of two of these classes showed no class-specific amino acids among the mammalian species examined. The gene belonging to the third class encoded an isoprotein which was clearly distinct, and members of this class may play a unique role in vivo. Sequencing of the three alpha-tubulin genes was also undertaken in CMR795, a colcemid-resistant clonal CHO cell line which has previously been shown to have structural and functional alterations in its tubulin proteins. We found differences in the tubulin nucleotide sequence compared with the parental line; however, no differences in the alpha-tubulin proteins encoded in the two cell lines were observed.

Comparison of the late H1 histone genes of the sea urchins Lytechinus pictus and Strongelocentrotus purpuratus

We have isolated and sequenced a gene encoding a late H1 histone subtype from the sea urchin species L. pictus. The primary structure of the late H1 subtype encoded by this gene is 209 amino acids in length, and has a net positive charge of 67. This gene is present in a single copy per haploid genome and encodes an mRNA of 752 nucleotides. Late H1 transcripts are detected in the unfertilized egg and are most prevalent in gastrulating embryos. Comparison of 375 bp of 5' flanking sequences of the L. pictus late H1 gene and the H1-gamma gene of a distantly related sea urchin species, S. purpuratus, reveals large blocks of sequences that are identical between the two genes. To determine if these conserved 5' sequences are present in other members of the sea urchin H1 gene family, the analogous region of S. purpuratus H1-alpha, an early H1 gene, was sequenced. The homology between the flanking sequences of the early and late families was limited to consensus sequences which are found upstream of all H1 genes. The possible regulatory implications of these findings are discussed.

Complete sequence of three alpha-tubulin cDNAs in Chinese hamster ovary cells: each encodes a distinct alpha-tubulin isoprotein

The genome of Chinese hamster ovary (CHO) cells contains a complex family of approximately 16 alpha-tubulin genes, many of which may be pseudogenes. We present here the complete cDNA sequences of three expressed alpha-tubulin genes; one of these genes has been identified only in CHO cells. The noncoding regions of these three CHO alpha-tubulin genes differed significantly, but their coding regions were highly conserved. Nevertheless, we observed differences in the predicted amino acid sequences for the three genes. A comparison of the CHO alpha-tubulin sequences with all of the sequences available for mammals allowed assignment of the alpha-tubulin genes to three classes. The proteins encoded by the members of two of these classes showed no class-specific amino acids among the mammalian species examined. The gene belonging to the third class encoded an isoprotein which was clearly distinct, and members of this class may play a unique role in vivo. Sequencing of the three alpha-tubulin genes was also undertaken in CMR795, a colcemid-resistant clonal CHO cell line which has previously been shown to have structural and functional alterations in its tubulin proteins. We found differences in the tubulin nucleotide sequence compared with the parental line; however, no differences in the alpha-tubulin proteins encoded in the two cell lines were observed.