Model system for evaluation of alternative splicing: exon skipping

Mouse Amelogenin Exons 8 and 9: Sequence Analysis and Protein Distribution

Amelogenin is the major protein of the developing enamel. Two additional exons, termed 8 and 9, have been characterized in the rat. Our aim was: to identify the mouse amelogenin exons 8/9 sequences; to investigate the potential presence of the alternative spliced isoforms of amelogenin exons 8/9; and to immunolocalize proteins containing sequences encoded by exons 8/9 during odontogenesis. RT-PCR analysis with exon 9 anti-sense primer generated 2 major amplicons with the use of a mouse tooth cDNA library and dental cell lines. DNA sequence analysis showed 93% identify with the rat exons 8/9 sequence. Alternative splicing of exon 3 was also found, but only in cDNAs lacking exons 8 and 9. Immunohistochemistry localized exons 8/9-encoded proteins in ameloblasts, young odontoblasts, and stratum intermedium cells. Analysis of our data supports the hypothesis that: (1) AMELX contains 2 additional exons; (2) ameloblasts and odontoblasts synthesize amelogenin 8/9; and (3) amelogenin splice variants may have unique functions during tooth formation.

Identification and characterization of the cDNA sequence encoding amelogenin in rabbit (Oryctolagus cuniculus)

Amelogenins, the most abundant proteins in tooth enamel extracellular matrix (ECM), are essential for tooth amelogenesis. The nucleotide sequence of amelogenin gene (AMEL) for rabbit, as an important member of mammals and good continuously growing incisor model, is important for comparative and evolutional study. Previous studies about rabbit amelogenin proteins got no consensus yet even as to their existence or size. In this study, with combined usage of in silico and molecular cloning technologies, we identified sequences of two transcripts of rabbit amelogenin, resulting from the alternative splicing of the 45-bp exon 4. The coding regions of the two transcripts are of 567- and 522-bp, encoding 188 and 173 amino acids including a 17-residue signal peptide, respectively. Sequence analysis revealed that rabbit amelogenin features in extremely high GC-content in nucleotide sequence and Alanine content in protein sequence. Detailed comparison of amino acid sequence with other mammals showed that the rabbit amelogenin protein is conserved in the sites and regions important for protein functions. Overall, our results uncovered the mysteries about rabbit amelogenin and revealed its sequence peculiarities.

SR proteins ASF/SF2 and SRp55 participate in tissue factor biosynthesis in human monocytic cells

BACKGROUND

Human monocytes express two naturally occurring forms of circulating tissue factor (TF) - full-length TF, a membrane-spanning protein, and alternatively spliced TF, a soluble molecule. Presence of the variable exon 5 in TF mRNA determines whether the encoded TF protein is transmembrane, or soluble. Recently, an essential SR protein ASF/SF2 was implicated in TF pre-mRNA processing in human platelets.

OBJECTIVE

To examine molecular mechanisms governing regulated processing of TF pre-mRNA in human monocytic cells.

METHODS AND RESULTS

In silico analysis of the human TF exon 5, present only in full-length TF mRNA, revealed putative binding motifs termed exonic splicing enhancers (ESE) for the SR proteins ASF/SF2 and SRp55, which were found to be abundantly expressed in monocytic cell lines THP-1 and SC, as well as monocyte-enriched peripheral blood mononuclear cells (PBMC). Using a splice competent mini-gene reporter system transiently expressed in monocytic cells, it was determined that weakening of either five closely positioned ASF/SF2 ESE (bases 87-117) or a single conserved SRp55 ESE (base 39) results in severe skipping of exon 5. ASF/SF2 and SRp55 were found to physically associate with the identified ESE.

CONCLUSIONS

SR proteins ASF/SF2 and SRp55 appear to interact with the variable TF exon 5 through ESE at bases 39 and 87-117. Weakening of the above ESE modulates splicing of TF exon 5. This study is the first to identify and experimentally characterize cis-acting splicing elements involved in regulated biosynthesis of human TF.

Validation of amelogenesis imperfecta inferred from amelogenin evolution

We used the evolutionary analysis of amelogenin (AMEL) in 80 amniotes (52 mammalian and 28 reptilian sequences) to aid in the genetic diagnosis of X-linked amelogenesis imperfecta (AIH1). Out of 191 residues, 77 were found to be unchanged in mammals, and only 34 in amniotes. The latter are considered crucial residues for enamel formation, while the 43 residues conserved only in mammals could indicate that they play new, important roles for enamel formation in this lineage. The 5 substitutions leading to AIH1 were validated when the mammalian dataset was used, and 4 of them with the amniote dataset. These 2 sequence datasets will facilitate the validation of any human AMEL mutation suspected of involvement in AIH1. This evolutionary analysis also revealed numerous residues that appeared to be important for correct AMEL function, but their role remains to be elucidated.

Amelogenin-mediated regulation of osteoclastogenesis, and periodontal cell proliferation and migration

We previously reported that amelogenin isoforms M180 and leucine-rich amelogenin peptide (LRAP) are expressed in the periodontal region, and that their absence is associated with increased cementum defects in amelogenin-knockout (KO) mice. The aim of the present study was to characterize the functions of these isoforms in osteoclastogenesis and in the proliferation and migration of cementoblast/periodontal ligament cells. The co-cultures of wild-type (WT) osteoclast progenitor and KO cementoblast/periodontal ligament cells displayed more tartrate-resistant acid phosphatase (TRAP)-positive cells than the co-cultures of WT cells. The addition of LRAP to both co-cultures significantly reduced RANKL expression and the TRAP-positive cells. Proliferation and migration rates of the KO cementoblast/periodontal ligament cells were lower than those of WT cells and increased with the addition of either LRAP or P172 (a porcine homolog of mouse M180). Thus, we demonstrate the regulation of osteoclastogenesis by LRAP, and the proliferation and migration of cementoblast/periodontal ligament cells by LRAP and P172.

Identification of the Expressed Form of Human Cytosolic Phospholipase A2β (cPLA2β)

In this study, we identify the principal splice variant of human cytosolic phospholipase A(2)beta (cPLA(2)beta) (also known as Group IVB cPLA(2)) present in cells. In human lung, spleen, and ovary and in a lung epithelial cell line (BEAS-2B), cPLA(2)beta is expressed as a 100-kDa protein, not the 114-kDa form originally predicted. Using RNA interference, the 100-kDa protein in BEAS-2B cells was confirmed to be cPLA(2)beta. BEAS-2B cells contain three different RNA splice variants of cPLA(2)beta (beta1, beta2, and beta3). cPLA(2)beta1 is identical to the previously cloned cPLA(2)beta, predicted to encode a 114-kDa protein. However, cPLA(2)beta2 and cPLA(2)beta3 splice variants are smaller and contain internal deletions in the catalytic domain. The 100-kDa cPLA(2)beta in BEAS-2B cells is the translated product of cPLA(2)beta3. cPLA(2)beta3 exhibits calcium-dependent PLA(2) activity against palmitoyl-arachidonyl-phosphatidylethanolamine and low level lysophospholipase activity but no activity against phosphatidylcholine. Unlike Group IVA cPLA(2)alpha, cPLA(2)beta3 is constitutively bound to membrane in unstimulated cells, localizing to mitochondria and early endosomes. cPLA(2)beta3 is widely expressed in tissues, suggesting that it has a generalized function at these unique sites.

Identification of temporal and spatial expression patterns of amelogenin isoforms during mouse molar development

Amelogenin synthesis is initiated in a restricted time frame during odontogenesis. Polypeptides translated from several alternatively spliced isoforms of amelogenin mRNA have been identified in ameloblasts and odontoblasts. Recent studies suggest that the isoforms deleting exons 6a, 6b, and 6c produce polypeptides that might exert regulatory functions governing the late stages of ameloblast and odontoblast differentiation. Herein, the spatial and temporal expression of mouse amelogenin mRNA isoforms M194, M180, M73, and M59 have been determined around the perinatal development period using splice form-specific probes. Expression levels and distribution patterns varied with developmental stage and cell location. Amelogenin mRNA expression was most prominent within the enamel organ at boundaries between cell layers, beginning at the newborn stage (PN0.5). Odontoblasts supported the expression of M73 and M59 mRNA from developmental stages PN0.5 to PN1.5 (1 d of age). In contrast, ameloblasts expressed predominantly the M180 mRNA isoform with full exon 6 but devoid of exon 4. In the enamel organ, the stratum intermediun cells supported expression of the full-length isoform, M194, including the full exon 6 and exon 4 sequences, and strikingly, expression of M180 message was inhibited. In conclusion, ameloblasts, odontoblasts, and stratum intermedium cells demonstrate selective alternative splicing patterns of the amelogenin pre-mRNA transcript.

Amelogenin: lessons from evolution

Amelogenin plays a crucial role in enamel structure and mineralization, but the function of its various domains is far to be understood. Evolutionary analysis seems to be a promising way to approach structure/function relationships. In this paper, we review the knowledge of amelogenin with a particular focus on what we have learnt from evolution, and we bring new data on the origin and evolution of this molecule. The comparison of amniote (reptiles and mammals) amelogenin sequences reveals that, in contrast to the well-conserved C- and N-terminal domains, the central region (most of exon 6) is highly variable. The evolutionary analysis indicates that it was created by repeated insertion of three amino acids (triplets ProXGlu or ProXX). In several mammalian lineages a new run of triplet insertions and deletions has occurred independently in a locus considered a hot spot of mutation for mammalian amelogenin. In lizard and snake amelogenin evolves rapidly. Sequence alignment reveals that several residues in the N- and C-terminal regions were kept unchanged during 250 million years (MY), proving their importance for amelogenin structure and function. This alignment permits a rapid validation of the amelogenin mutations in human. Genome sequencing and gene mapping permitted to refine the amelogenin story, in relation to the common location (chromosome 4 in human) of several genes coding for dental proteins and SPARCL1, a SPARC (osteonectin) relative. Amelogenin shares a similar organisation with these genes and a blast search in databanks indicates a strong relationship between amelogenin, ameloblastin and enamelin. Taken together these data suggest that amelogenin could have originated from either ameloblastin or enamelin, themselves being created from SPARCL1, which itself originated from a SPARC duplication, 600 millions years ago.

Molecular evolution of amelogenin in mammals

An evolutionary analysis of mammalian amelogenin, the major protein of forming enamel, was conducted by comparison of 26 sequences (including 14 new ones) representative of the main mammalian lineages. Amelogenin shows highly conserved residues in the hydrophilic N- and C-terminal regions. The central hydrophobic region (most of exon 6) is more variable, but it has conserved a high amount of proline and glutamine located in triplets, PXQ, indicating that these residues play an important role. This region evolves more rapidly, and is less constrained, than the other well-conserved regions, which are subjected to strong constraints. The comparison of the substitution rates in relation to the CpG richness confirmed that the highly conserved regions are subjected to strong selective pressures. The amino acids located at important sites and the residues known to lead to amelogenesis imperfecta when substituted were present in all sequences examined. Evolutionary analysis of the variable region of exon 6 points to a particular zone, rich in either amino acid insertion or deletion. We consider this region a hot spot of mutation for the mammalian amelogenin. In this region, numerous triplet repeats (PXQ) have been inserted recently and independently in five lineages, while most of the hydrophobic exon 6 region probably had its origin in several rounds of triplet insertions, early in vertebrate evolution. The putative ancestral DNA sequence of the mammalian amelogenin was calculated using a maximum likelihood approach. The putative ancestral protein was composed of 177 residues. It already contained all important amino acid positions known to date, its hydrophobic variable region was rich in proline and glutamine, and it contained triplet repeats PXQ as in the modern sequences.

Leucine-rich amelogenin peptide: a candidate signaling molecule during cementogenesis

BACKGROUND

Cementum is a critical mineralized tissue; however, control of its formation remains undefined. One hypothesis is that enamel matrix proteins/peptides secreted by ameloblasts and/or epithelial rest cells contribute to the control of cementum formation via epithelial-mesenchymal interactions. Here, we focused on determining whether or not leucine-rich amelogenin peptide (LRAP), translated from an alternatively spliced amelogenin RNA, altered cementoblast behavior.

METHODS

Immortalized murine cementoblasts (OCCM-30) were exposed to LRAP and evaluated for: 1) proliferative activity; 2) gene expression using Northern blot for Cbfal (core binding factor alpha-1); OCN (osteocalcin), OPN (osteopontin), and real-time reverse transcription-polymerase chain reaction (RT-PCR) for OPG (osteoprotegerin); and RANKL (receptor activator of NF-kappaB ligand); 3) signaling pathway using inhibitors of PKA (THFA), PKC (GF109203X), and MAPK (UO126); and 4) mineralization evaluated by von Kossa and Alizarin-red.

RESULTS

LRAP had no effect on cell proliferation up to 6 days, with a decrease in cell growth observed at the highest dose by 9 days versus untreated cells. LRAP down regulated OCN and up regulated OPN in a dose- and time-response fashion, and inhibited the capacity of mineral nodule formation. Transcripts for OPG were increased in LRAP-treated cells compared to control, but RANKL mRNA levels were not affected. Core binding factor alpha (Cbfa) mRNA, expressed constitutively, was not affected by LRAP. Signaling pathway assays suggested involvement of the MAPK pathway, since the addition of the MAPK inhibitor suppressed OPN expression in LRAP-treated cells.

CONCLUSION

Leucine-rich amelogenin peptide appears to have a direct effect on cementoblast activity that may prove significant during development as well as in regeneration of periodontal tissues.