Genomic organisation, alternative splicing and primary structure of human matrilin-4

Matrilins

Marilins mediate interactions between macromolecular components of the extracellular matrix, e.g., collagens and proteoglycans. They are composed of von Willebrand factor type A and epidermal growth factor-like domains and the subunits oligomerize via coiled-coil domains. Matrilin-1 and -3 are abundant in hyaline cartilage, whereas matrilin-2 and -4 are widespread but less abundant. Mutations in matrilin genes have been linked to chondrodysplasias and osteoarthritis and recently characterization of matrilin-deficient mice revealed novel functions in mechanotransduction, regeneration, or inflammation. Due to their intrinsic adhesiveness and partially also low abundance, the study of matrilins is cumbersome. In this chapter, we describe methods for purification of matrilins from tissue, analysis of matrilins in tissue extracts, recombinant expression, and generation of matrilin-specific antibodies.

Replacement of Rbpj with Rbpjl in the PTF1 complex controls the final maturation of pancreatic acinar cells

BACKGROUND & AIMS

The mature pancreatic acinar cell is dedicated to the production of very large amounts of digestive enzymes. The early stages of pancreatic development require the Rbpj form of the trimeric Pancreas Transcription Factor 1 complex (PTF1-J). As acinar development commences, Rbpjl gradually replaces Rbpj; in the mature pancreas, PTF1 contains Rbpjl (PTF1-L). We investigated whether PTF1-L controls the expression of genes that complete the final stage of acinar differentiation.

METHODS

We analyzed acinar development and transcription in mice with disrupted Rbpjl (Rbpjl(ko/ko) mice). We performed comprehensive analyses of the messenger RNA population and PTF1 target genes in pancreatic acinar cells from these and wild-type mice.

RESULTS

In Rbpjl(ko/ko) mice, acinar differentiation was incomplete and characterized by decreased expression (as much as 99%) of genes that encode digestive enzymes or proteins of regulated exocytosis and mitochondrial metabolism. Whereas PTF1-L bound regulatory sites of genes in normal adult pancreatic cells, the embryonic form (PTF1-J) persisted in the absence of Rbpjl and replaced PTF1-L; the extent of replacement determined gene expression levels. Loss of PTF1-L reduced expression (>2-fold) of only about 50 genes, 90% of which were direct targets of PTF1-L. The magnitude of the effects on individual digestive enzyme genes correlated with the developmental timing of gene activation. Absence of Rbpjl increased pancreatic expression of liver-restricted messenger RNA.

CONCLUSIONS

Replacement of Rbpj by Rbpjl in the PTF1 complex drives acinar differentiation by maximizing secretory protein synthesis, stimulating mitochondrial metabolism and cytoplasmic creatine-phosphate energy stores, completing the packaging and secretory apparatus, and maintaining acinar-cell homeostasis.

Proteolytic processing causes extensive heterogeneity of tissue matrilin forms

The matrilins are a family of multidomain extracellular matrix proteins with adapter functions. The oligomeric proteins have a bouquet-like structure and bind to a variety of different ligands whereby the avidity of their interactions is dependent on the number of subunits and domains present. Here we show the contribution of post-translational proteolytic processing to the heterogeneity of matrilins seen in tissue extracts and cell culture supernatants. A cleavage site after two glutamate residues in the hinge region close to the C-terminal coiled-coil oligomerization domain is conserved among the matrilins. Cleavage at this site yields molecules that lack almost complete subunits. The processing is least pronounced in matrilin-1 and particularly complex in matrilin-2, which contains additional cleavage sites. Replacement of the hinge region in matrilin-4 by the matrilin-1 hinge region had no marked effect on the processing. A detailed study revealed that matrilin-4 is processed already in the secretory pathway and that the activation of the responsible enzymes is dependent on proprotein convertase activity. Matrilin-3 and -4, but not matrilin-1 subunits present in matrilin-1/-3 hetero-oligomers, were identified as substrates for ADAMTS4 and ADAMTS5, whereas ADAMTS1 did not cleave any matrilin. A neo-epitope antibody raised against the N terminus of the C-terminal cleavage product of matrilin-4 detected processed matrilin-4 in cultures of primary chondrocytes as well as on cartilage sections showing that the conserved cleavage site is used in vivo.

Comparative gene expression profile analysis between native human odontoblasts and pulp tissue

AIM

To undertake a large-scale analysis of the expression profiles of native human pulp tissue and odontoblasts, and search for genes expressed only in odontoblasts.

METHODOLOGY

Microarray was performed to pooled pulp and odontoblasts of native human third molars and to pooled +/- TGF-beta1 cultured pulps and odontoblasts (137 teeth). The repeatability of microarray analysis was estimated by comparing the experimental pulp samples with expression profiles of two pulp samples downloaded from the GEO database. The genes expressed only in the experimental pulp samples or in odontoblasts were divided into categories, and the expression of selected odontoblast-specific genes of extracellular matrix (ECM) organization and biogenesis category was confirmed with RT-PCR and Western blot.

RESULTS

A 85.3% repeatability was observed between pulp microarrays, demonstrating the high reliability of the technique. Overall 1595 probe sets were positive only in pulp and 904 only in odontoblasts. Sixteen expressed sequence tags (ESTs), which represent transcribed sequences encoding possibly unknown genes, were detected only in odontoblasts; two consistently expressed in all odontoblast samples. Matrilin 4 (MATN4) was the only ECM biogenesis and organization related gene detected in odontoblasts but not in pulp by microarray and RT-PCR. MATN4 protein expression only in odontoblasts was confirmed by Western blot.

CONCLUSIONS

Pulp tissue and odontoblast gene expression profiling provides basic data for further, more detailed protein analysis. In addition, MATN4 and the two ESTs could serve as an odontoblast differentiation marker, e.g. in odontoblast stem cell research.

Abnormal collagen fibrils in cartilage of matrilin-1/matrilin-3-deficient mice

Matrilins are oligomeric extracellular matrix adaptor proteins mediating interactions between collagen fibrils and other matrix constituents. All four matrilins are expressed in cartilage and mutations in the human gene encoding matrilin-3 (MATN3) are associated with different forms of chondrodysplasia. Surprisingly, however, Matn3-null as well as Matn1- and Matn2-null mice do not show an overt skeletal phenotype, suggesting a dominant negative pathomechanism for the human disorders and redundancy/compensation among the family members in the knock-out situation. Here, we show that mice lacking both matrilin-1 and matrilin-3 develop an apparently normal skeleton, but exhibit biochemical and ultrastructural abnormalities of the knee joint cartilage. At the protein level, an altered SDS-PAGE band pattern and a clear up-regulation of the homotrimeric form of matrilin-4 were evident in newborn Matn1/Matn3 and Matn1 knock-out mice, but not in Matn3-null mice. The ultrastructure of the cartilage matrix after conventional chemical fixation was grossly normal; however, electron microscopy of high pressure frozen and freeze-substituted samples, revealed two consistent observations: 1) moderately increased collagen fibril diameters throughout the epiphysis and the growth plate in both single and double mutants; and 2) increased collagen volume density in Matn1(-/-)/Matn3(-/-) and Matn3(-/-) mice. Taken together, our results demonstrate that matrilin-1 and matrilin-3 modulate collagen fibrillogenesis in cartilage and provide evidence that biochemical compensation might exist between matrilins.

Cloning and characterization of rat importin 9: implication for its neuronal function

We describe the structure of the rat importin 9 gene, together with its transcripts and the encoded protein with its putative functional domains. The importin 9 gene contains 24 exons in a genomic region spanning >52,000 bp. It is transcribed into two mRNAs, generated by means of alternative polyadenylation site usage arranged in tandem. Both transcripts possess the same noncanonical polyadenylation signal (AGUAAA) in rat, this hexamer being conserved in all vertebrates examined. Additionally, intron 8 is bordered by AT-AC dinucleotides. Importin 9 is expressed throughout adult rat tissues, but the 114-kDa Importin 9 protein was detected only in the brain. The localization of the Importin 9 protein was examined by immunohistochemistry in both adult rat tissues and primary hippocampal cell cultures. The strongest labeling was detected in vivo in areas populated by neurons in high density and also in the dendritic processes emanating from these cells. This protein was clearly concentrated in the nuclei of these cells, although their cytoplasms too were heavily labeled. Strong cytoplasmic and very strong nuclear staining was found in a vast majority of the cells with neuronal morphology in vitro. Cultured cells with glial morphology generally exhibited a weaker cytoplasmic labeling. In these cells, the signal decorated the nuclear envelope without nuclear staining and gradually dwindled toward the cell periphery. These results hint at the cell- or tissue-type specific functions of this type of importin protein.

Zebrafish (Danio rerio) matrilins: shared and divergent characteristics with their mammalian counterparts

We have cloned the cDNAs of the zebrafish (Danio rerio) members of the matrilin family of extracellular adaptor proteins. In contrast to mammals, no orthologue of matrilin-2 was found in zebrafish, either by RT (reverse-transcriptase) PCR using degenerated primers or by screening the databases (Ensembl and NCBI); however, two forms of matrilin-3, matrilin-3a and -3b, were present. The identity with the mammalian matrilins is from more than 70% for the VWA (von Willebrand factor A)-like domains to only 28% for the coiled-coil domains of matrilin-3a and -3b. In all zebrafish matrilins we found a greater variety of splice variants than in mammals, with splicing mainly affecting the number of EGF (epidermal growth factor)-like repeats. The exon-intron organization is nearly identical with that of mammals, and also the characteristic AT-AC intron interrupting the exons coding for the coiled-coil domain is conserved. In the matrilin-3b gene a unique exon codes for a proline- and serine/threonine-rich domain, possibly having mucin-like properties. The matrilin-1 and -3a genes were mapped to chromosome 19 and 20 respectively by the radiation hybrid method. The temporal and spatial expression of zebrafish matrilins is similar to that seen in the mouse. Zebrafish matrilin-4 is highly expressed as early as 24 hpf (h post fertilization), whereas the other matrilins show peak expression at 72 hpf. By immunostaining of whole mounts and sections, we found that matrilin-1 and -3a show predominantly skeletal staining, whereas matrilin-4 is more widespread, with the protein also being present in loose connective tissues and epithelia.

Expression of matrilin-2 in human skin

The extracellular matrix is composed of a large number of different modular proteins. Matrilin-2 is a newly described member of the protein superfamily with von Willebrand factor A-like modules. To examine the expression of matrilin-2 in human skin, the distribution of protein and mRNA was studied by immunohistochemistry and in situ hybridization. In addition, immunoblotting and real-time reverse transcription polymerase chain reaction were used to investigate the expression of matrilin-2 in keratinocyte and fibroblast cultures. In vivo, keratinocytes and fibroblasts were both found to express matrilin-2 mRNA and deposit the protein at the basal side of the dermal-epidermal basement membrane. Matrilin-2 molecules synthesized by the two cell types in vitro appeared to be processed differently by cell-associated proteases. Transcription of matrilin-2 mRNA in keratinocytes was enhanced by a diffusible factor produced by fibroblasts, suggesting a regulatory mechanism for the production of extracellular matrix at the dermal-epidermal junction. These findings demonstrate that matrilin-2 is expressed in normal skin by keratinocytes and fibroblasts and may thus contribute to cutaneous homeostasis.

Characterization of the matrilin coiled-coil domains reveals seven novel isoforms

Matrilins constitute a family of four oligomeric extracellular proteins that are involved in the development and homeostasis of cartilage and bone. To reveal their homo- and heterotypic oligomerization propensities, we analyzed the four human matrilin coiled-coil domains by biochemical and biophysical methods. These studies not only confirmed the homo- and heterotypic oligomerization states reported for the full-length proteins but revealed seven novel matrilin isoforms. Specific heterotrimeric interactions of variable chain stoichiometries were observed between matrilin-1 and matrilin-2, matrilin-1 and matrilin-4, and matrilin-2 and matrilin-4. In addition, matrilin-1 formed two different specific heterotetramers with matrilin-3. Interestingly, a distinct heterotrimer consisting of three different chains was formed between matrilin-1, matrilin-2, and matrilin-4. No interactions, however, were observed between matrilin-2 and matrilin-3 or between matrilin-3 and matrilin-4. Both homo- and heterotypic oligomers folded into parallel disulfide-linked structures, although coiled-coil formation was not dependent on disulfide bridge formation. Our results indicate that the heterotypic preferences seen for the matrilin coiled-coil domains are the result of the packing of the hydrophobic core rather than ionic interactions. Mass spectrometry revealed that the concentrations of the individual chains statistically determined the stoichiometry of the heteromers, suggesting that formation of the different matrillin chain combinations is controlled by expression levels.

Comparative analysis of the mouse and human genes (Matn2 and MATN2) for matrilin-2, a filament-forming protein widely distributed in extracellular matrices

We previously identified matrilin-2 (MATN2), the largest member of the novel family of matrilins. These filament-forming adapter proteins expressed in a distinct, but partially overlapping, pattern in all tissues were implicated in the organization of the extracellular matrix. Matrilin-2 functions in a great variety of tissues. Here, we present the genomic organization of the highly conserved mouse and human MATN2 loci, which cover >100 kb and 167.167 kb genomic regions, respectively, and are composed of 19 exons. RT-PCR analysis revealed that alternative transcripts with identical protein coding regions are transcribed from two promoters in both species. The upstream, housekeeping type promoter is functional in all tissues and cell types tested. The activity of the downstream, TATA-like promoter preceded with putative motifs for the homeobox transcription factor PRRX2 is restricted to embryonic fibroblasts and certain cell lines. The oligomerization module is split by an U12-type AT-AC intron found in conserved position in all four matrilin genes. We assigned Matn2 to mouse chromosome 15, linked to Trhr and Sntb1 in a region synthenic to human chromosome 8q22-24.

Characterization of the mouse matrilin-4 gene: a 5' antiparallel overlap with the gene encoding the transcription factor RBP-l

We have isolated and characterized the gene encoding mouse matrilin-4 (Matn4), an extracellular matrix protein present in a broad spectrum of tissues. The gene spanned 16 kb, consisted of 12 exons, and localized to chromosome 2. As in all known matrilin genes, the last intron, separating the exons coding for the coiled-coil domain, did not follow the GT-AG rule and belonged to the subgroup of introns having AT-AC at the ends. Matn4 contained two exons in the 5' UTR that could be alternatively spliced. We localized a major and a minor transcription start site to two different untranslated exons: exon 0a and exon 0b. Matn4 divergently overlapped 5' with the gene encoding RBP-L (for recombining binding protein suppressor of hairless-like; Rbpsuhl), a transcription factor with homology to RBP-JK. Exon 1 of Rbpsuhl was located in the second intron of Matn4, whereas exon 0a, the first exon of Matn4, was located in the second intron of Rbpsuhl. The second exons of the respective genes overlapped in an antisense orientation. We mapped the major transcription start of Rbpsuhl to a position approximately 150 nt upstream of the splice acceptor site of the first intron, leading to the synthesis of a truncated variant of RBP-L probably missing the amino-terminal 121 amino acid residues. We analyzed the expression of the different Matn4 and Rbpsuhl transcripts by quantitative RT-PCR; this showed the highest expression for both genes in lung and brain. In situ hybridization of brain sections showed a partially overlapping expression pattern for the two genes.

Molecular structure, processing, and tissue distribution of matrilin-4

Matrilin-4 is the most recently identified member of the matrilin family of von Willebrand factor A-like domain containing extracellular matrix adapter proteins. Full-length matrilin-4 was expressed in 293-EBNA cells, purified using affinity tags, and subjected to biochemical characterization. The largest oligomeric form of recombinantly expressed full-length matrilin-4 is a trimer as shown by electron microscopy, SDS-polyacrylamide gel electrophoresis, and mass spectrometry. Proteolytically processed matrilin-4 species were also detected. The cleavage occurs in the short linker region between the second von Willebrand factor A-like domain and the coiled-coil domain leading to the release of large fragments and the formation of dimers and monomers of intact subunits still containing a trimeric coiled-coil. In immunoblots of calvaria extracts similar degradation products could be detected, indicating that a related proteolytic processing occurs in vivo. Matrilin-4 was first observed at day 7.5 post-coitum in mouse embryos. Affinity-purified antibodies detect a broad expression in dense and loose connective tissue, bone, cartilage, central and peripheral nervous systems and in association with basement membranes. In the matrix formed by cultured primary embryonic fibroblasts, matrilin-4 is found in a filamentous network connecting individual cells.

Molecular Properties of Matrilin-3 Isolated from Human Growth Cartilage

Matrilin-3 is a recently identified matrix protein of cartilage that shows sequence homology to matrilin-1 (cartilage matrix protein or CMP). Here we identify and characterize the molecular properties of matrilin-3 from human growth cartilage by immunochemical and mass spectrometry methods. Extracts of fetal skeletal cartilage were resolved by SDS-PAGE and candidate matrilin subunits were identified by electrospray mass spectrometry of tryptic peptides. Matrilin-3 and matrilin-1 were both present in disulfide-bonded tetrameric components. Polyclonal antisera to synthetic peptides specific to each subunit confirmed the identities by Western blotting and further demonstrated the existence of several forms of tetramer. A homotetramer (matrilin-3)4 and more than one species of heterotetramer containing matrilin-3 and matrilin-1 chains were resolved. Immunohistochemistry of tissue sections confirmed that both matrilin-1 and matrilin-3 are widely codistributed throughout human skeletal growth cartilage.

Molecular structure and tissue distribution of matrilin-3, a filament-forming extracellular matrix protein expressed during skeletal development

Matrilin-3 is a recently identified member of the superfamily of proteins containing von Willebrand factor A-like domains and is able to form hetero-oligomers with matrilin-1 (cartilage matrix protein) via a C-terminal coiled-coil domain. Full-length matrilin-3 and a fragment lacking the assembly domain were expressed in 293-EBNA cells, purified, and subjected to biochemical characterization. Recombinantly expressed full-length matrilin-3 occurs as monomers, dimers, trimers, and tetramers, as detected by electron microscopy and SDS-polyacrylamide gel electrophoresis, whereas matrilin-3, purified from fetal calf cartilage, forms homotetramers as well as hetero-oligomers of variable stoichiometry with matrilin-1. In the matrix formed by cultured chondrosarcoma cells, matrilin-3 is found in a filamentous, collagen-dependent network connecting cells and in a collagen-independent pericellular network. Affinity-purified antibodies detect matrilin-3 expression in a variety of mouse cartilaginous tissues, such as sternum, articular, and epiphyseal cartilage, and in the cartilage anlage of developing bones. It is found both inside the lacunae and in the interterritorial matrix of the resting, proliferating, hypertrophic, and calcified cartilage zones, whereas the expression is lower in the superficial articular cartilage. In trachea and in costal cartilage of adult mice, an expression was seen in the perichondrium. Furthermore, matrilin-3 is found in bone, and its expression is, therefore, not restricted to chondroblasts and chondrocytes.

The matrilins: a novel family of oligomeric extracellular matrix proteins

The matrilin family at present has four members that all share a structure made up of von Willebrand factor A domains, epidermal growth factor-like domains and a coiled coil alpha-helical module. The first member of the family, matrilin-1 (previously called cartilage matrix protein or CMP), is expressed mainly in cartilage. Matrilin-3 has a similar tissue distribution, while matrilin-2 and -4 occur in a wide variety of extracellular matrices. Matrilin-1 is associated with cartilage proteoglycans as well as being a component of both collagen-dependent and collagen-independent fibrils and on the basis of the related structures other matrilins may play similar roles. The matrilin genes are strictly and differently regulated and their expression may serve as markers for cellular differentiation.