A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus.

Biomineralization, the biologically controlled formation of mineral deposits, is of widespread importance in biology, medicine, and engineering. Mineralized structures are found in most metazoan phyla and often have supportive, protective, or feeding functions. Among deuterostomes, only echinoderms and vertebrates produce extensive biomineralized structures. Although skeletons appeared independently in these two groups, ancestors of the vertebrates and echinoderms may have utilized similar components of a shared genetic "toolkit" to carry out biomineralization. The present study had two goals. First, we sought to expand our understanding of the proteins involved in biomineralization in the sea urchin, a powerful model system for analyzing the basic cellular and molecular mechanisms that underlie this process. Second, we sought to shed light on the possible evolutionary relationships between biomineralization in echinoderms and vertebrates. We used several computational methods to survey the genome of the purple sea urchin Strongylocentrotus purpuratus for gene products involved in biomineralization. Our analysis has greatly expanded the collection of biomineralization-related proteins. We have found that these proteins are often members of small families encoded by genes that are clustered in the genome. Most of the proteins are sea urchin-specific; that is, they have no apparent homologues in other invertebrate deuterostomes or vertebrates. Similarly, many of the vertebrate proteins that mediate mineral deposition do not have counterparts in the S. purpuratus genome. Our findings therefore reveal substantial differences in the primary sequences of proteins that mediate biomineral formation in echinoderms and vertebrates, possibly reflecting loose constraints on the primary structures of the proteins involved. On the other hand, certain cellular and molecular processes associated with earlier events in skeletogenesis appear similar in echinoderms and vertebrates, leaving open the possibility of deeper evolutionary relationships.

Expression of spicule matrix proteins in the sea urchin embryo during normal and experimentally altered spiculogenesis.

During its embryonic development, the sea urchin embryo forms an endoskeletal calcitic spicule. This instance of biomineralization is experimentally accessible and also offers the advantage of occurring within a developmental context. Here we investigate the time course of appearance and localization of two proteins among the four dozen that constitute the protein matrix of the skeletal spicule. SM50 and SM30 have been studied in some detail, and polyclonal antisera have been prepared against them (C. E. Killian and F. H. Wilt, 1996, J. Biol. Chem. 271, 9150-9159). Using these antibodies we describe here the localization and time course of accumulation of these two proteins in Strongylocentrotus purpuratus, both in the intact embryo and in micromere cultures. We also investigate the disposition of the matrix proteins, SM50, SM30, and PM27, in the three-dimensional spicule by studying changes in protein localization during experimental manipulation of isolated skeletal spicules. We conclude that SM50, PM27, and SM30 probably play different roles in biomineralization, based on their localization and patterns of expression. It is unlikely that these proteins are solely structural elements within the mineral. SM50 and PM27 may play a role in defining the extracellular space in which spicule deposition occurs, while SM30 may play a role in secretion of spicule components. Finally, we report on the effects of serum on expression of some primary mesenchyme-specific proteins in micromere cultures; withholding serum severely depresses accumulation of SM30 but has only modest effects on the accumulation of other proteins.

Spfkh1 encodes a transcription factor implicated in gut formation during sea urchin development.

A member of the forkhead class of transcription factors from sea urchins (Spfkh1) that is expressed specifically in the endoderm of developing embryos has been identified. Spfkh1 was expressed transiently in the embryo, with peak levels of messenger ribonucleic acid (mRNA) accumulating at the time endoderm invaginated into the interior of the embryo. Expression was limited to the invaginating endoderm in the early gastrula, then became further restricted to the base of the invaginating gut at the mid-gastrula stage. Expression diminished by the end of gastrulation. This expression pattern indicates that Spfkh1 mRNA accumulates in endodermal cells as they invaginate, but disappears rapidly in endodermal cells that undergo convergent extension. Treatment of embryos during cleavage stages with lithium or phorbol esters caused an increase in Spfkh1 mRNA accumulation and expanded the domain of expression of Spfkh1, suggesting that signaling through the inositol-tris-phosphate protein kinase C (IP3-PKC) signaling pathway is upstream of Spfkh1 expression. The expression pattern of Spfkh1 suggests that it is centrally involved in specification and/or differentiation of the gut. Disruption of the extracellular matrix (ECM) prevents formation of the gut, but does not inhibit initiation of Spfkh1 expression. Embryos arrested prior to gastrulation continued to express Spfkh1 well past the time it was down-regulated in normal embryos, suggesting the ECM or cell movement is required for the decrease in Spfkh1 mRNA during gastrulation.

Expression of spicule matrix protein gene SM30 in embryonic and adult mineralized tissues of sea urchin Hemicentrotus pulcherrimus.

We have isolated a cDNA clone for spicule matrix protein, SM30, from sea urchin Hemicentrotus pulcherrimus and have studied the expression of this gene in comparison with that of another spicule matrix protein gene, SM50. In cultured micromeres as well as in intact embryos transcripts of SM30 were first detectable around the onset of spicule formation and rapidly increased with the growth of spicules, which accompanied accumulation of glycosylated SM30 protein(s). When micromeres were cultured in the presence of Zn2+, spicule formation and SM30 expression were suppressed, while both events resumed concurrently after the removal of Zn2+ from the culture medium. Expression of SM50, in contrast, started before the appearance of spicules and was not sensitive to Zn2+. Differences were also observed in adult tissues; SM30 mRNA was detected in spines and tube feet but not in the test, while SM50 mRNA was apparent in all of these mineralized tissues at similar levels. These results strongly suggest that the SM30 gene is regulated by a different mechanism to that of the SM50 gene and that the products of these two genes are differently involved in sea urchin biomineralization. A possible role of SM30 protein in skeleton formation is discussed.

Characterization of the proteins comprising the integral matrix of Strongylocentrotus purpuratus embryonic spicules.

In the present study, we enumerate and characterize the proteins that comprise the integral spicule matrix of the Strongylocentrotus purpuratus embryo. Two-dimensional gel electrophoresis of [35S]methionine radiolabeled spicule matrix proteins reveals that there are 12 strongly radiolabeled spicule matrix proteins and approximately three dozen less strongly radiolabeled spicule matrix proteins. The majority of the proteins have acidic isoelectric points; however, there are several spicule matrix proteins that have more alkaline isoelectric points. Western blotting analysis indicates that SM50 is the spicule matrix protein with the most alkaline isoelectric point. In addition, two distinct SM30 proteins are identified in embryonic spicules, and they have apparent molecular masses of approximately 43 and 46 kDa. Comparisons between embryonic spicule matrix proteins and adult spine integral matrix proteins suggest that the embryonic 43-kDa SM30 protein is an embryonic isoform of SM30. An adult 49-kDa spine matrix protein is also identified as a possible adult isoform of SM30. Analysis of the SM30 amino acid sequences indicates that a portion of SM30 proteins is very similar to the carbohydrate recognition domain of C-type lectin proteins.

Genomic organization of a gene encoding the spicule matrix protein SM30 in the sea urchin Strongylocentrotus purpuratus.

We report the characterization of a genomic clone containing portions of two tandemly arranged genes that encode a spicule matrix protein, SM30, of the sea urchin Strongylocentrotus purpuratus. The isolated 18.4-kilo-base genomic clone contains the complete genomic sequence of one SM30 gene, designated SM30-alpha, and a portion of another SM30 gene, designated SM30-beta. Southern blot analysis shows that SM30 protein is encoded by a small gene family of two to four members. RNase protection assays indicate that the SM30-alpha gene is expressed at the time of spicule formation in the sea urchin embryo. In addition, mapping of SM30-alpha shows that a large single intron interrupts the coding sequence. Comparison of the nucleic acid and amino acid sequences of the SM30-alpha genomic sequence and the previously isolated SM30 cDNA reveals them to be very similar, but not identical. We also demonstrate that 2.6 kilobases of upstream sequence of SM30-alpha are sufficient to direct primary mesenchyme cell-specific expression of a reporter gene construct.

Characterization and expression of a gene encoding a 30.6-kDa Strongylocentrotus purpuratus spicule matrix protein.

We describe here the isolation and characterization of several cDNA clones that encode a single 30.6-kDa Strongylocentrotus purpuratus spicule matrix protein designated SM30. The clones were isolated by screening a lambda gt11 cDNA library with a rabbit polyclonal antiserum raised against S. purpuratus total spicule matrix proteins. DNA sequencing reveals that the SM30 protein is acidic. RNA blot analysis shows that the cDNAs hybridize to a single 1.8-kb transcript and that there is a sharp increase in the SM30 transcript levels at middle to late mesenchyme blastula stage. SM30 transcript levels remain high through the 3-day pluteus stage. In situ hybridization analysis indicates that, within the embryo, SM30 transcript accumulation is restricted to the primary mesenchyme cells. Quantitations of SM30 transcript levels show that by the prism stage there are about 29,000 SM30 transcripts present per embryo, which averages to approximately 480 transcripts per primary mesenchyme cell. Additionally, RNA blot analysis of total RNA isolated from adult tissues shows that SM30 mRNA accumulates exclusively in mineralized tissues. These findings taken together strongly suggest that the gene corresponding to the SM30 cDNAs does in fact encode a spicule matrix protein.

The accumulation and translation of a spicule matrix protein mRNA during sea urchin embryo development.

In this report we further characterize the expression of the gene that encodes the 50-kDa spicule matrix protein (SM50) during development of the sea urchin Strongylocentrotus purpuratus. Quantitative measurements of SM50 mRNA levels using the single-stranded probe excess titration technique indicate that SM50 transcript levels attain a maximum level of 8000 to 10,000 transcripts per embryo by the gastrula stage, representing 120 to 200 SM50 mRNAs per primary mesenchyme cell. Experiments analyzing run-on transcription in nuclei isolated at different stages of development indicate that the sharp increase in SM50 mRNA levels occurring at the time of primary mesenchyme ingression is concomitant with an increase in transcription of the SM50 gene. We have also analyzed the RNA sequences present on polyribosomes at different stages of development. These studies indicate that SM50 mRNA is present on polyribosomes as soon as it begins to accumulate (which is well in advance of overt spicule formation) and SM50 mRNA remains on polyribosomes through subsequent development. From estimates of the rate of SM50 protein synthesis based on these data, we calculated that the maximum amount of SM50 accumulated during development through the 4-day pluteus stage is approximately 7.4 pg/embryo. This approximation is concordant with the amount of SM50 actually found in the sea urchin embryo.

Ribonucleoside uptake and phosphorylation during fertilization and early development of the sea-urchin, Strongylocentrotus purpuratus.

Uptake of the four ribonucleosides normally present in RNA increases nearly 50-fold shortly after fertilization in eggs of the sea-urchin, Strongylocentrotus purpuratus. Uridine, adenosine and cytidine are phosphorylated (greater than 95%) to their mono-, di- and triphosphates immediately after transport into the fertilized egg. Although guanosine is transported to an extent equal to the other three ribonucleosides, less than 12% of its phosphorylated after transport. In vitro nucleoside and nucleotide kinase assays of unfertilized egg homogenates indicate that the uridine, adenosine and cytidine kinases as well as the uridylate, adenylate, cytidylate and guanylate kinases are present in the egg prior to fertilization. Substrate competition measurements indicate that adenosine phosphorylation is catalyzed by a monospecific enzyme, while uridine and cytidine phosphorylations are catalyzed by a common kinase. Guanosine kinase activity was not detectable in unfertilized egg homogenates. Between 3 h and 5 h after fertilization the phosphorylation of transported guanosine begins to increase as it enters the embryo. By 7 h after fertilization, more than 95% of the guanosine entering the embryo is phosphorylated to the mono-, di- and triphosphates. More than 80% is phosphorylated to guanosine triphosphate. The timing of increased guanosine phosphorylation correlates with a decrease in the acid-soluble GTP pools in the embryo, suggesting that increased guanosine kinase activity is a response to increased GTP demand. These results, in view of the importance of GTP in many cellular processes, imply a crucial role for guanosine kinase activation in GTP pool maintenance and cellular metabolism during early sea-urchin development.

Effects of aphidicolin on premature condensation of sperm chromosomes in fertilized sea urchin eggs.

Unfertilized Strongylocentrotus purpuratus eggs may be treated with ammonia to initiate maternal DNA replication and the maternal cell cycle. When these eggs are polyspermically fertilized 75 min after the beginning of ammonia treatment, the nuclei of the fertilizing spermatozoa undergo premature chromosome condensation (PCC) in an apparent attempt to conform to the advanced maternal cell cycle. PCC is inhibited if maternal DNA replication is blocked by exposing the eggs to aphidicolin but will proceed if this exposure begins after replication is complete. Additionally, PCC will proceed in ammonia-activated, polyspermically fertilized anucleate merogons in the continuous presence of aphidicolin. These results suggest that the direct inhibitory effect of aphidicolin may well be limited to the replication of DNA and that the unreplicated maternal nucleus itself exerts negative control over the development of chromosome-condensing conditions in the maternal cytoplasm.

Increased uptake of thymidine in the activation of sea urchin eggs. III. Effects of aphidicolin.

Uptake and phosphorylation of externally supplied [3H]-thymidine are fully stimulated in fertilized sea urchin eggs exposed to 5.0 micrograms/ml aphidicolin. As in untreated controls, the rate of uptake in aphidicolin-treated eggs increases greater than 50-fold shortly after fertilization, and greater than 85% of the transported thymidine is immediately phosphorylated to the triphosphate. The intracellular levels of [3H]-thymidine triphosphate (3H-dTTP) resulting from an external supply of [3H]-thymidine is therefore equal in aphidicolin-treated and untreated fertilized eggs. Under the same experimental conditions, the incorporation of externally supplied [3H]-thymidine into newly synthesized DNA of fertilized eggs is 90% inhibited by exposure to aphidicolin. The full availability of 3H-dTTP in these eggs further suggests that aphidicolin inhibits specifically at the level of DNA synthesis. This inhibitory effect is proportional to the concentration of aphidicolin between 0 and 5.0 micrograms/ml. In the continuous presence of 5.0 micrograms/ml aphidicolin, fertilized eggs fail to undergo mitotic chromosome condensation, nuclear envelope breakdown, and cytokinesis, suggesting a dependent link between these processes and the completion of nuclear DNA synthesis.