Distribution and Function of the Nacrein-Related Proteins Inferred from Structural Analysis

Nacrein is the first identified molluscan organic matrix (OM) component considered to be specifically involved in nacreous layer formation (Miyamoto et al. in Proc Natl Acad Sci USA 93:9657–9660, 1996); however, its localization in shell microstructures and phylogeny of molluscs and function still remain unclear. Therefore, to elucidate the functions of the nacrein-related proteins, we set up three experiments focused on (1) the primary structure of the nacrein-related proteins, (2) the tertiary structure of nacrein, and (3) in vitro crystallization of the proteins. In regard to the first experiment, our Western blot analysis and cDNA cloning clearly indicated for the first time the common occurrence of nacrein-related proteins both biochemically and genetically, independent of molluscan phylogeny and shell microstructures. Together with the data reported so far, we classified nacrein-related proteins into four types. Second, we determined the overall structure of nacrein via small-angle x-ray scattering via the program DAMMIN. This kind of research has never yet been attempted for the molluscan OM proteins. Our results inferred the structure of nacrein to be N-shaped based on the low-resolution solution dummy atom model structures that could be derived from the presence of the NG-repeat domain that was intercalated into two CA domains. Third, the result of the crystallization experiment revealed inhibitory activity of crystal formation for nacrein-related proteins when present in free state but the same molecule, when attached to the ISM, may regulate the form and size of aragonite crystal. These results demonstrate the fundamentally important function of nacrein-related proteins in molluscan shell formation. The nucleotide sequences reported in this article have been submitted to GenBank^TK/DDBJ with accession numbers AB252479 to AB252484.     

Expression of genes responsible for biomineralization of Pinctada fucata during development

This study compares the expression levels of nacrein, N16, MSI60, Prismalin-14, aspein and MSI31 genes during the ontogeny of Pinctada fucata. Several novel findings were obtained: 1) The early calcitic prismatic layer was distinguished as a thin membrane-like structure. 2) Initial formation of the nacreous layer started from the mantle pallial region at the age of 31 days. 3) 18S rRNA of P. fucata was determined to be more suitable as a real-time PCR reference gene compared with GAPDH and β-actin genes. 4) A relationship was recognized between the expression levels of the above six organic matrix genes and biomineralization of the larval shell. The lack of calcite in the shells of the veliger and pediveliger stages, when MSI31 and Prismalin-14 genes were expressed, makes a role of polymorph control by these genes less likely. The hypothetical involvement of N16 and MSI60 proteins in aragonitic nacreous layer formation was corroborated by the expression levels of N16 and MSI60 genes during ontogeny. Our results are important with respect to the control of CaCO₃ crystal polymorphism and shell microstructures in P. fucata.     

Expression of biomineralisation genes in tissues and cultured cells of the abalone Haliotis tuberculata

Mollusc shell biomineralisation involves a variety of organic macromolecules (matrix proteins and enzymes) that control calcium carbonate (CaCO₃) deposition, growth of crystals, the selection of polymorph, and the microstructure of the shell. Since the mantle and the hemocytes play an important role in the control of shell formation, primary cell cultures have been developed to study the expression of three biomineralisation genes recently identified in the abalone Haliotis tuberculata: a matrix protein, Lustrin A, and two carbonic anhydrase enzymes. Mantle cells and hemocytes were successfully maintained in primary cultures and were evaluated for their viability and proliferation over time using a semi-automated assay (XTT). PCR and densitometric analysis were used to semi-quantify the gene expression and compare the level of expression in native tissues and cultured cells. The results demonstrated that the three genes of interest were being expressed in abalone tissues, with expression highest in the mantle and much lower in the hemocytes and the gills. Biomineralisation genes were also expressed significantly in mantle cells, confirming that primary cultures of target tissues are suitable models for in vitro investigation of matrix protein secretion.     

Molecular Evolution and Functionally Important Structures of Molluscan Dermatopontin: Implications for the Origins of Molluscan Shell Matrix Proteins

A major shell matrix protein originally obtained from a freshwater snail is a molluscan homologue of Dermatopontins, a group of Metazoan proteins also called TRAMP (tyrosine-rich acidic matrix protein). We sequenced and identified 14 molluscan homologues of Dermatopontin from eight snail species belonging to the order Basommatophora and Stylommatophora. The bassommatophoran Dermatopontins fell into three types, one is suggested to be a shell matrix protein and the others are proteins having more general functions based on gene expression analyses. N-glycosylation is inferred to be important for the function involved in shell calcification, because potential N-glycosylation sites were found exclusively in the Dermatopontins considered as shell matrix proteins. The stylommatophoran Dermatopontins fell into two types, also suggested to comprise a shell matrix protein and a protein having a more general function. Phylogenetic analyses using maximum likelihood and Bayesian methods revealed that gene duplication events occurred independently in both basommatophoran and stylommatophoran lineages. These results suggest that the dermatopontin genes were co-opted for molluscan calcification at least twice independently after the divergence of basommatophoran and stylommatophoran lineages, or more recently than we have expected. [Reviewing Editor: Dr. David Pollock]     

Multiple ferritin subunit genes of the Pacific oyster Crassostrea gigas and their distinct expression patterns during early development

Multiple ferritin subunit genes are reported in mollusks, but they have not been systematically classified. Based on the recently published whole genome sequence, we screened out the four ferritin subunit genes (cgi-fer1–cgi-fer4) from the Pacific oyster Crassostrea gigas. The four genes were predicted to encode two non-secretory and two secretory peptides. Further phylogenetic analyses revealed two groups of non-secretory and secretory ferritin subunits in mollusks. This differs dramatically from the situation in mammals or insects, which contain only non-secretory or secretory ferritin subunits. These results emphasize the evolution of molluscan ferritin subunit genes. The expression patterns of the four genes during early development exhibited dramatic differences, indicating the functional diversity of these genes. Among them, cgi-fer2 was the only gene expressed prevalently and is thus suggested to be the major house-keeping ferritin subunit gene. The expression of the other three genes was tissue-specific beginning in the D-veliger stage. Based on their expression patterns, we inferred important functions of cgi-fer2 in ciliated tissues and of the other three genes in the digestive system. Moreover, our results indicated potentially different roles of ferritin subunit genes during larval shell formation in gastropods and bivalves, which may be helpful in understanding the molecular mechanisms that cause the different shells of gastropods and bivalves. In addition, we conducted a further semi-quantitative analysis of the four genes in four major developmental stages and five adult tissues. The results also revealed dramatically different expression patterns of the genes, which brought additional functional indications. This work may promote studies on molluscan ferritins and shed light on the evolution of ferritin subunit genes among different animal groups.     

In-depth proteomic analysis of a mollusc shell: acid-soluble and acid-insoluble matrix of the limpet Lottia gigantea

Background

Invertebrate biominerals are characterized by their extraordinary functionality and physical properties, such as strength, stiffness and toughness that by far exceed those of the pure mineral component of such composites. This is attributed to the organic matrix, secreted by specialized cells, which pervades and envelops the mineral crystals. Despite the obvious importance of the protein fraction of the organic matrix, only few in-depth proteomic studies have been performed due to the lack of comprehensive protein sequence databases. The recent public release of the gastropod Lottia gigantea genome sequence and the associated protein sequence database provides for the first time the opportunity to do a state-of-the-art proteomic in-depth analysis of the organic matrix of a mollusc shell.

Results

Using three different sodium hypochlorite washing protocols before shell demineralization, a total of 569 proteins were identified in Lottia gigantea shell matrix. Of these, 311 were assembled in a consensus proteome comprising identifications contained in all proteomes irrespective of shell cleaning procedure. Some of these proteins were similar in amino acid sequence, amino acid composition, or domain structure to proteins identified previously in different bivalve or gastropod shells, such as BMSP, dermatopontin, nacrein, perlustrin, perlucin, or Pif. In addition there were dozens of previously uncharacterized proteins, many containing repeated short linear motifs or homorepeats. Such proteins may play a role in shell matrix construction or control of mineralization processes.

Conclusions

The organic matrix of Lottia gigantea shells is a complex mixture of proteins comprising possible homologs of some previously characterized mollusc shell proteins, but also many novel proteins with a possible function in biomineralization as framework building blocks or as regulatory components. We hope that this data set, the most comprehensive available at present, will provide a platform for the further exploration of biomineralization processes in molluscs.     

Die Paläobiochemie,ein neues Arbeitsgebiet der Evolutionsforschung

Attention is focussed on a novel tool to study evolutionary trends in organisms. Emphasis is placed on the comparative biochemistry of shell proteins. It is tentatively concluded that the organic matrix of molluscan shells is predominantly a mixture of “secreted” collagen and k-m-e-f type proteins, and to a lesser extent of mucopolysaccharides. Each species has its characteristic organic pattern. Thus, the heterogeneity of calcified tissues can be related to molluscan phylogeny and evolution.     

A new high-throughput AFLP approach for identification of new genetic polymorphism in the genome of the clonal microorganism Mycobacterium tuberculosis

We have here applied high-throughput amplified fragment length polymorphism (htAFLP) analysis to strains belonging to the five classical species of the Mycobacterium tuberculosis complex. Using 20 strains, three enzyme combinations and eight selective amplification primer pairs, 24 AFLP reactions were performed per strain. Overall, this resulted in 480 DNA fingerprints and more than 1200 htAFLP-amplified PCR fragments were visualised per strain. The cumulative dendrogram correctly clustered strains from the various species, albeit within a distance of 6.5% for most of them. The single isolate of Mycobacterium canettii presented separately at 19% distance. All over, 169 fragments (14%) appeared to be polymorphic. Sixty-eight were specific for M. canetti and forty-five for Mycobacterium bovis. For the 10 different M. tuberculosis strains included in the present analysis, 56 polymorphic markers were identified. Upon sequencing 20 of these marker regions and comparisons with the H37Rv genome sequence, 25% appeared to share homology to members of the antigenically variable PE/PPE surface protein encoding gene family confirming previous findings on the genetic heterogeneity within these genes. In addition, homologues for phage genes and insertion element-encoded genes were detected. Forty-five percent of the sequences derived from ORFs with a currently unknown function, which was corroborated by genome sequence comparison for the clinical M. tuberculosis CD 1551 isolate. Sequence variation in M. tuberculosis was assessed in more detail for a subset of these loci by newly designed PCR restriction fragment length polymorphism (RFLP) tests and direct sequencing. Fourteen novel PCR RFLP tests were developed and twelve novel single nucleotide polymorphisms (SNPs) were identified, all suited for epidemiological analysis of M. tuberculosis. The tests allowed for identification of the major Mycobacterium species and M. tuberculosis variants and clones.     

Molecular mechanism of the nacreous layer formation in Pinctada maxima

We have cloned the cDNAs that encode two kinds of molluscan shell matrix proteins, namely N66 and N14, in the nacreous layer of Pinctada maxima. N66 is composed of carbonic anhydrase-like and repeat domains, as described for nacrein (1) in the pearls of P. fucata. N14 is homologous to N16, recently found in the nacreous layer of P. fucata (2) and is characterized by high proportions of Gly, Tyr, and Asn together with NG repeat sequences. The molecular weights of these proteins were estimated as 59,814 and 13,734 Da, respectively. Structural differences were clearly indicated in the alignment and length of the repeat sequences of the sets of the homogeneous proteins (N66/nacrein and N14/N16). The longer repeat sequences of N66 and N14 may be responsible for P. maxima's excellent property of calcification. The in vitro crystallization experiments revealed that the mixture of N66 and N14 could induce platy aragonite layers highly similar to the nacreous layer, once adsorbed onto the membrane of the water-insoluble matrix.     

Involvement of Hox genes in shell morphogenesis in the encapsulated development of a top shell gastropod (Gibbula varia L.)

Regulatory gene expression during the patterning of molluscan shells has only recently drawn the attention of scientists. We show that several Hox genes are expressed in association with the shell gland and the mantle in the marine vetigastropod Gibbula varia (L.). The expression of Gva-Hox1, Gva-Post2, and Gva-Post1 is initially detected in the trochophore larval stage in the area of the shell field during formation of embryonic shell. Later, during development, these genes are expressed in the mantle demonstrating their continuous role in larval shell formation and differentiation of mantle edge that secretes the adult shell. Gva-Hox4 is expressed only late during the development of the veliger-like larva and may also be involved in the adult shell morphogenesis. Additionally, this gene also seems to be associated with secretion of another extracellular structure, the operculum. Our data provide further support for association of Hox genes with shell formation which suggest that the molecular mechanisms underlying shell synthesis may consist of numerous conserved pattern-formation genes. In cephalopods, the only other molluscan class in which Hox gene expression has been studied, no involvement of Hox genes in shell formation has been reported. Thus, our results suggest that Hox genes are coopted to various functions in molluscs.     

A genome-wide survey of R gene polymorphisms in Arabidopsis

We used polymorphism analysis to study the evolutionary dynamics of 27 disease resistance (R) genes by resequencing the leucine-rich repeat (LRR) region in 96 Arabidopsis thaliana accessions. We compared single nucleotide polymorphisms (SNPs) in these R genes to an empirical distribution of SNP in the same sample based on 876 fragments selected to sample the entire genome. LRR regions are highly polymorphic for protein variants but not for synonymous changes, suggesting that they generate many alleles maintained for short time periods. Recombination is also relatively common and important for generating protein variants. Although none of the genes is nearly as polymorphic as RPP13, a locus previously shown to have strong signatures of balancing selection, seven genes show weaker indications of balancing selection. Five R genes are relatively invariant, indicating young alleles, but all contain segregating protein variants. Polymorphism analysis in neighboring fragments yielded inconclusive evidence for recent selective sweeps at these loci. In addition, few alleles are candidates for rapid increases in frequency expected under directional selection. Haplotype sharing analysis revealed significant underrepresentation of R gene alleles with extended haplotypes compared with 1102 random genomic fragments. Lack of convincing evidence for directional selection or selective sweeps argues against an arms race driving R gene evolution. Instead, the data support transient or frequency-dependent selection maintaining protein variants at a locus for variable time periods.     

Proteomic analysis of the organic matrix of the abalone <Emphasis Type="Italic">Haliotis asinina</Emphasis> calcified shell

Background  

The formation of the molluscan shell is regulated to a large extent by a matrix of extracellular macromolecules that are secreted by the shell forming tissue, the mantle. This so called "calcifying matrix" is a complex mixture of proteins and glycoproteins that is assembled and occluded within the mineral phase during the calcification process. While the importance of the calcifying matrix to shell formation has long been appreciated, most of its protein components remain uncharacterised.     

Genetic map of nine polymorphic loci comprising a single linkage group on rat chromosome 10: evidence for linkage conservation with human chromosome 17 and mouse chromosome 11.

Seven genes and two anonymous markers were mapped to a single linkage group on rat chromosome 10 using progeny of an F2 intercross of Fischer (F344/N) and Lewis (LEW/N) inbred rats. Two genes, the neu oncogene or cellular homologue of the viral oncogene erbb2 (ERBB2) and growth hormone (GH) were mapped by Southern blot analysis of restriction fragment length polymorphisms. Five genes, embryonic skeletal myosin heavy chain (MYH3), androgen binding protein/sex hormone binding globulin (SHBG), asialoglycoprotein receptor (hepatic lectin)-1 (ASGR1), ATP citrate lysase (CLATP), and pancreatic polypeptide (PPY), and two anonymous markers, F16F2 and F10F1, were mapped using PCR amplification techniques. The PCR-typable polymorphic markers for the five genes were also highly polymorphic in 10 other inbred rat strains (SHR/N, WKY/N, MNR/N, MR/N, LOU/MN, BN/SsN, BUF/N, WBB1/N, WBB2/N, and ACI/N). These markers should be useful in genetic analysis of traits described in inbred rat strains, as well as in genetic monitoring of such strains. The loci in this linkage group covered 50 cM of rat chromosome 10 with the following order: MYH3, SHBG/ASGR1 (no recombinants detected), F16F2, ERBB2, CLATP, PPY, GH, and F10F1. Comparative gene mapping analysis indicated that this region of rat chromosome 10 exhibits linkage conservation with regions of human chromosome 17 and mouse chromosome 11.