Proteomic and Transcriptomic Analyses in the Slipper Snail Crepidula fornicata Uncover Shell Matrix Genes Expressed During Adult and Larval Biomineralization.

The gastropod shell is a composite composed of minerals and shell matrix proteins (SMPs). SMPs have been identified by proteomics in many molluscs, but few have been studied in detail. Open questions include (1) what gene regulatory networks regulate SMP expression, (2) what roles individual SMPs play in biomineralization, and (3) how the complement of SMPs changes over development. These questions are best addressed in a species in which gene perturbation studies are available; one such species is the slipper snail, Crepidula fornicata. Here, SEM and pXRD analysis demonstrated that the adult shell of C. fornicata exhibits crossed lamellar microstructure and is composed of aragonite. Using high-throughput proteomics we identified 185 SMPs occluded within the adult shell. Over half of the proteins in the shell proteome have known biomineralization domains, while at least 10% have no homologs in public databases. Differential gene expression analysis identified 20 SMP genes that are up-regulated in the shell-producing mantle tissue. Over half of these 20 SMPs are expressed during development with two, CfSMP1 and CfSMP2, expressed exclusively in the shell gland. Together, the description of the shell microstructure and a list of SMPs now sets the stage for studying the consequences of SMP gene knockdowns in molluscs.

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.

Special evolutionary properties of genes encoding a protein with a simple amino acid repeat.

We have examined the evolution of a gene, SM50, encoding a component of the spicule matrix, which plays an integral role in the formation of the echinoderm skeleton. This gene was originally characterized in Strongylocentrotus purpuratus and encodes an imperfect tandem repeat of six or seven amino acids. We have analyzed the sequence of this repeat in a number of sea urchin species and have determined that the repeat regions have undergone concerted evolution. There are differences in the repeat region between species, but the overall repeat structure is conserved, suggesting the repeat forms a structural domain important in biomineralization. The inherent conserved amino acid repeat structure promotes concerted evolution due to the high probability of misreplication and unequal crossing-over in the repeated segment of the gene. While there are constraints on the amino acids allowed in the repeat region, there are also variations, so that the sequences observed illustrate the balance between amino acid substitutions and concerted evolution. We have evidence that substitutions can alter the mechanisms of unequal crossing-over, altering the way concerted evolution occurs. The way in which concerted evolution occurred appears to be determined by the degree of sequence similarity between the repeats in a given gene, which influences how unequal crossing over may occur. We have mapped the differences in repeat regions on existing phylogenetic trees and indicate where concerted evolution has taken place. We also confirm an earlier report that Hemicentrotus pulcherrimus fits into the Strongylocentrotus genus and examine the evolution of the H. pulcherrimus SM50 repeat relative to other members of this genus.

A sea urchin genome project: sequence scan, virtual map, and additional resources.

Results of a first-stage Sea Urchin Genome Project are summarized here. The species chosen was Strongylocentrotus purpuratus, a research model of major importance in developmental and molecular biology. A virtual map of the genome was constructed by sequencing the ends of 76,020 bacterial artificial chromosome (BAC) recombinants (average length, 125 kb). The BAC-end sequence tag connectors (STCs) occur an average of 10 kb apart, and, together with restriction digest patterns recorded for the same BAC clones, they provide immediate access to contigs of several hundred kilobases surrounding any gene of interest. The STCs survey >5% of the genome and provide the estimate that this genome contains approximately 27,350 protein-coding genes. The frequency distribution and canonical sequences of all middle and highly repetitive sequence families in the genome were obtained from the STCs as well. The 500-kb Hox gene complex of this species is being sequenced in its entirety. In addition, arrayed cDNA libraries of >10(5) clones each were constructed from every major stage of embryogenesis, several individual cell types, and adult tissues and are available to the community. The accumulated STC data and an expanding expressed sequence tag database (at present including >12, 000 sequences) have been reported to GenBank and are accessible on public web sites.

Conservation of the WD-repeat, microtubule-binding protein, EMAP, in sea urchins, humans, and the nematode C. elegans.

The echinoderm microtubule-associated protein (EMAP) is the most abundant microtubule-binding protein in the first cleavage mitotic apparatus in sea urchin embryos. The first goal of this study was to determine whether there is sufficient EMAP in the egg and embryo to modify microtubule dynamics during the early cleavages divisions and whether EMAP functions at a specific time or place in the embryo. To accomplish this goal, we examined the relative abundance, tissue distribution, and temporal pattern of EMAP expression during embryonic development. The second goal of this study was to identify important functional domains within the EMAP coding sequence. A conserved sequence might reveal a potential microtubule-binding domain. We cloned, sequenced and compared overlapping EMAP cDNAs from two different sea urchin species that diverged approximately 80 million years ago, and compared these with cDNA sequences from a vertebrate and nematode species. From quantitative immunoblots, we determined the EMAP concentration in eggs to be 4 microM. The steady-state levels of EMAP mRNA and protein accumulated during development, and all three germ layers expressed EMAP. During the early stages of development, EMAP and tubulin were both abundant in the ectoderm, mesoderm and endoderm. However, during late gastrulation and the formation of the early pluteus larvae, EMAP was enriched in the mesoderm, while tubulin staining was most abundant in the archenteron. These results indicate that EMAP may have tissue-specific functions in the late stage embryo. To identify conserved functional domains, we compared the predicted amino acid sequence encoded by Strongylocentrotus purpuratus and Lytechinus variegatus EMAP cDNAs, and determined that these two sea urchin EMAPs were 95% conserved and shared an identical domain organization. A parsimonious analysis of these sea urchin protein sequences, as well as human and C. elegans EMAP sequences was used to construct a gene tree. Together these results suggest that EMAP is an important microtubule protein required at all developmental stages of sea urchins, and whose cellular function may be conserved amongst metazoans.

Characterization of a gene encoding a developmentally regulated winged helix transcription factor of the sea urchin Strongylocentrotus purpuratus.

Spfkh1 is a Strongylocentrotus purpuratus transcription factor that contains a winged helix DNA binding domain. Both the gene and overlapping cDNAs encoding this factor have been cloned and completely sequenced. We have mapped the start of transcription by primer extension to a site 600 base pairs 5' to the start of translation. Spfkh1 is transcribed in one open reading frame that contains the DNA binding domain, nuclear localization signal and transactivation domain. The deduced amino acid sequence encodes a 40. 7kDa protein with a pI of 9.96. Alignments of the DNA binding domain with other forkhead domains reveal that this gene falls into Class II of the winged helix transcription factors. We have identified a unique carboxyl-terminal motif of unknown function that is present in all winged helix Class II transcription factors. A phylogenetic analysis of the DNA binding domains shows that, within the Class II, Spfkh1 groups with the deuterostomes as opposed to the protostomes. Analysis of the sequence 5' to the start of translation revealed binding sites for a large number of different transcription factors, many of which are present in multiple copies. The constellation of binding sites in the cis-regulatory region indicates that Spfkh1 is regulated by a complex set of factors, some of which are known to be endoderm specific. Included among these are binding sites for factors downstream of the Wnt/beta-catenin and hedgehog signaling pathways, implicating these pathways in both regulation of Spfkh1 and specification of endoderm.

Protein tyrosine kinase activity following fertilization is required to complete gastrulation, but not for initial differentiation of endoderm and mesoderm in the sea urchin embryo.

The egg activation process functions to implement developmental programs that act much later in embryogenesis. One example of this is the fact that application of protein tyrosine kinase inhibitors to the fertilized sea urchin egg for a 15-min period results in a defect in the gastrulation process occurring over 24 h later (Kinsey, W. H., Dev. Biol. 172, 704-707, 1995). In the present study, we show that the window of sensitivity is not due to differential uptake of inhibitor, and establish that the inhibitor inhibits tyrosine kinase activity at the time of application. We also demonstrate that inhibition of protein tyrosine kinase activity in the zygote causes a specific defect in the morphogenetic movements associated with gastrulation without interfering with the initial specification and differentiation of endoderm and mesoderm. Differentiation events occurring concurrent with or subsequent to gastrulation were also suppressed in embryos derived from treated zygotes. These findings indicate that fertilization initiates a signaling cascade involving protein tyrosine kinase activity that is required specifically for events at gastrulation. This signaling event is required to complete the developmental program of both endoderm and mesoderm, but is different from those events necessary for initial specification of endodermal and mesodermal cell fate.

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.

Cell interactions in invertebrate development.

By utilizing both genetics and physical manipulations, studies on invertebrate embryos have provided substantial information on how cell interactions influence cell fate during development. The picture emerging from these studies suggest that while there may be varied and intricate patterns of cell interactions during the development of different embryos, the signaling molecules that convey positional information across cell membranes have been highly conserved.

Phorbol esters alter cell fate during development of sea urchin embryos.

Protein kinase C (PKC) has been implicated as important in controlling cell differentiation during embryonic development. We have examined the ability of 12-O-tetradecanoyl phorbol-13-acetate (TPA), an activator of PKC, to alter the differentiation of cells during sea urchin development. Addition of TPA to embryos for 10-15 min during early cleavage caused dramatic changes in their development during gastrulation. Using tissue-specific antibodies, we have shown that TPA causes the number of cells that differentiate as endoderm and mesoderm to increase relative to the number that differentiate as ectoderm. cDNA probes show that treatment with TPA causes an increase in accumulation of RNAs specific to endoderm and mesoderm with a concomitant decrease in RNAs specific to ectoderm. Treatment of isolated prospective ectodermal cells with TPA causes them to differentiate into endoderm and mesoderm. The critical period for TPA to alter development is during early to mid cleavage, and treatment of embryos with TPA after that time has little effect. These results indicate that PKC may play a key role in determining the fate of cells during sea urchin development.

Characterization of a cDNA encoding a protein involved in formation of the skeleton during development of the sea urchin Lytechinus pictus.

In order to investigate the role of proteins in the formation of mineralized tissues during development, we have isolated a cDNA that encodes a protein that is a component of the organic matrix of the skeletal spicule of the sea urchin, Lytechinus pictus. The expression of the RNA encoding this protein is regulated over development and is localized to the descendents of the micromere lineage. Comparison of the sequence of this cDNA to homologous cDNAs from other species of urchin reveal that the protein is basic and contains three conserved structural motifs: a signal peptide, a proline-rich region, and an unusual region composed of a series of direct repeats. Studies on the protein encoded by this cDNA confirm the predicted reading frame deduced from the nucleotide sequence and show that the protein is secreted and not glycosylated. Comparison of the amino acid sequence to databases reveal that the repeat domain is similar to proteins that form a unique beta-spiral supersecondary structure.

Development and operation of the Wisconsin Research Network.

In 1987, the Wisconsin Academy of Family Physicians developed the Wisconsin Research Network (WReN) to support practice-based primary care research throughout Wisconsin. WReN has three objectives: to support the research efforts of individual physicians in community practices, to facilitate collaborative research among practicing physicians, and to provide academically based investigators with access to community practice sites. Due to a policy of actively encouraging membership, WReN has grown to 460 members during its 4-year history. Five WReN-supported papers have been published, and 22 state and national level presentations of WReN-supported research results have been made. Competitive grants totaling more than $2 million have been awarded to university-based investigators for studies using the resources of WReN. This paper describes the development, organization, and success of WReN as well as the challenges which must be addressed.

Determination of cell fate in sea urchin embryos.

Classical embryological studies have provided a great deal of information on the autonomy and stability of cell fate determination in early sea urchin embryos. However, these studies were limited by the tools available at the time, and the interpretation of the results of these experiments was limited by the lack of information available at the molecular level. Recent studies which have re-examined classical experiments at the molecular level have provided important new insights into the mechanism of determination in sea urchins, and require us to re-evaluate some long standing theories on the process of differentiation.

Range and stability of cell fate determination in isolated sea urchin blastomeres.

We have examined the developmental potential of blastomeres isolated from either the animal (mesomeres) or vegetal (macromeres-micromeres) half of 16-cell embryos of the sea urchin Lytechinus pictus. We have also examined the effects of two known vegetalizing agents on the development of isolated mesomeres; LiCl treatment and combination with micromeres, the small blastomeres found at the vegetal pole of the 16-cell embryo. The markers for differentiation used were both morphological (invaginations, spicules and pigment cells) and molecular (gut-specific alkaline phosphatase activity, and monoclonal antibodies against antigens specific for gut and oral ectoderm). Embryoids derived from isolated mesomeres expressed markers characteristic of vegetal differentiation only at very low levels. They did express an antigen characteristic of animal development, the oral ectoderm antigen, but with an altered pattern. Isolated macromere-micromere pairs expressed all markers characteristic of vegetal development, but did not express the marker characteristic of animal development. Increasing concentrations of LiCl caused isolated mesomeres to give rise to embryoids with an increasing tendency to express vegetal markers of differentiation, and it was found that expression of different vegetal markers begin to appear at different concentrations of LiCl. LiCl also caused the marker for oral ectoderm to be expressed in a more normal pattern. Combining micromeres with mesomeres also induced mesomere derivatives to differentiate in a vegetal manner. Micromeres were not completely effective in inducing a more normal pattern of expression of the marker for oral ectoderm. The treatment of isolated mesomeres with both LiCl and micromeres produces a synergistic effect resulting in embryoids expressing markers not induced by either treatment alone.

Lithium evokes expression of vegetal-specific molecules in the animal blastomeres of sea urchin embryos.

The mechanism of determination of early embryonic cells has been investigated using sea urchin embryos. An efficacious method of isolating blastomere pairs from the animal or vegetal half of sea urchin embryos was developed. The overt differentiation of separated animal and vegetal blastomere pairs resembles that of separated animal and vegetal hemispheres isolated by manual dissection. Treatment of animal blastomeres with LiCl caused them to display a morphology resembling that of isolated vegetal blastomeres. The effects of separation of animal and vegetal blastomeres and of treatment of animal blastomeres with LiCl were examined at the molecular level using gut alkaline phosphatase and a spicule matrix protein RNA as markers of differentiation. Histochemical staining and in situ hybridization studies showed that these markers are normally only expressed in vegetal blastomeres but that their expression can be evoked in animal blastomeres by treatment with LiCl.