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Genomic structure and alternative splicing of murine R2B receptor protein tyrosine phosphatases (PTPkappa, mu, rho and PCP-2).

Besco J, Popesco MC, Davuluri RV, Frostholm A, Rotter A - BMC Genomics (2004)

Bottom Line: The greatest variability in genomic organization and the majority of alternatively spliced exons were observed in the juxtamembrane domain, a region critical for the regulation of signal transduction.Comparison of the four R2B RPTP genes revealed virtually identical principles of genomic organization, despite great disparities in gene size due to variations in intron length.Although subtle differences in exon length were also observed, it is likely that functional differences among these genes arise from the specific combinations of exons generated by alternative splicing.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA. besco.1@osu.edu

ABSTRACT

Background: Four genes designated as PTPRK (PTPkappa), PTPRL/U (PCP-2), PTPRM (PTPmu) and PTPRT (PTPrho) code for a subfamily (type R2B) of receptor protein tyrosine phosphatases (RPTPs) uniquely characterized by the presence of an N-terminal MAM domain. These transmembrane molecules have been implicated in homophilic cell adhesion. In the human, the PTPRK gene is located on chromosome 6, PTPRL/U on 1, PTPRM on 18 and PTPRT on 20. In the mouse, the four genes ptprk, ptprl, ptprm and ptprt are located in syntenic regions of chromosomes 10, 4, 17 and 2, respectively.

Results: The genomic organization of murine R2B RPTP genes is described. The four genes varied greatly in size ranging from approximately 64 kb to approximately 1 Mb, primarily due to proportional differences in intron lengths. Although there were also minor variations in exon length, the number of exons and the phases of exon/intron junctions were highly conserved. In situ hybridization with digoxigenin-labeled cRNA probes was used to localize each of the four R2B transcripts to specific cell types within the murine central nervous system. Phylogenetic analysis of complete sequences indicated that PTPrho and PTPmu were most closely related, followed by PTPkappa. The most distant family member was PCP-2. Alignment of RPTP polypeptide sequences predicted putative alternatively spliced exons. PCR experiments revealed that five of these exons were alternatively spliced, and that each of the four phosphatases incorporated them differently. The greatest variability in genomic organization and the majority of alternatively spliced exons were observed in the juxtamembrane domain, a region critical for the regulation of signal transduction.

Conclusions: Comparison of the four R2B RPTP genes revealed virtually identical principles of genomic organization, despite great disparities in gene size due to variations in intron length. Although subtle differences in exon length were also observed, it is likely that functional differences among these genes arise from the specific combinations of exons generated by alternative splicing.

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Pairwise percentage nucleotide identity of individual exons. Exons 2–31 of the four murine R2B genes were compared in a pairwise fashion. Exon numbers are listed on the x axis, and the corresponding percentage identity for that exon is shown on the y axis. Three distinct regions may be discerned: The extracellular (exons 2–13), juxtamembrane (exons 14–18) and phosphatase (exons 19–32) domains.
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Figure 7: Pairwise percentage nucleotide identity of individual exons. Exons 2–31 of the four murine R2B genes were compared in a pairwise fashion. Exon numbers are listed on the x axis, and the corresponding percentage identity for that exon is shown on the y axis. Three distinct regions may be discerned: The extracellular (exons 2–13), juxtamembrane (exons 14–18) and phosphatase (exons 19–32) domains.

Mentions: Each of the R2B genes contained over 30 exons, which were examined pairwise to determine the overall nucleotide/exon identity between the four genes (Figure 7). Three major regions were delineated, each with varying degrees of sequence identity: Exons 2–13 comprised the extracellular segment (MAM, Ig and four fibronectin (FN) type III domains), exon 14–18 (juxtamembrane region), and exons 19–32 (two phosphatase domains). Although the number of exons comprising each of the extracellular domains was identical in each of the four genes, exon size varied in some domains and remained unchanged in others. Within the extracellular segment, the MAM domain showed the most extensive variation in exon size: The first exon ranged from 123 to 132 bp, and the third from 79 to 82bp (Figure 8). MAM domains are comprised of 160–170 amino acids containing four conserved cysteines; their function has been examined in some detail. When expressed in non-adherent cells, PTPμ [12-14] and PTPκ [15] proteins formed large calcium-independent clusters. Aggregation was strictly homophilic, consisting exclusively of cells expressing only a single R2B type [14-16]. Because this property had not been demonstrated with any of the other RPTP subfamilies, a crucial role for the MAM domain in this homophilic interaction was implied. However, in an in vitro binding assay in which regions of recombinant PTPμ were expressed [17], the homophilic binding site was localized to the immunoglobulin (Ig)-like domain. Subsequently, MAM and Ig domains were shown to function cooperatively in homophilic binding in both PTPμ and PTPκ [16]. It was suggested that the binding site is located in the Ig domain and the MAM domain is part of a "sorting" mechanism that confers homophilic binding specificity [6]. Figures 7 and 8 show that, when combined with the invariant 272 bp middle exon, each R2B MAM domain had a unique combination of exon sizes and low sequence identity, indicating a region of high specificity. The adjacent Ig-like domain contained exons of identical size, implying a less specific role than that of the MAM domain. These marked variations in sequence identity are consistent with the idea that the MAM domain plays a role in the mediation of homophilic binding specificity [6].


Genomic structure and alternative splicing of murine R2B receptor protein tyrosine phosphatases (PTPkappa, mu, rho and PCP-2).

Besco J, Popesco MC, Davuluri RV, Frostholm A, Rotter A - BMC Genomics (2004)

Pairwise percentage nucleotide identity of individual exons. Exons 2–31 of the four murine R2B genes were compared in a pairwise fashion. Exon numbers are listed on the x axis, and the corresponding percentage identity for that exon is shown on the y axis. Three distinct regions may be discerned: The extracellular (exons 2–13), juxtamembrane (exons 14–18) and phosphatase (exons 19–32) domains.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC373446&req=5

Figure 7: Pairwise percentage nucleotide identity of individual exons. Exons 2–31 of the four murine R2B genes were compared in a pairwise fashion. Exon numbers are listed on the x axis, and the corresponding percentage identity for that exon is shown on the y axis. Three distinct regions may be discerned: The extracellular (exons 2–13), juxtamembrane (exons 14–18) and phosphatase (exons 19–32) domains.
Mentions: Each of the R2B genes contained over 30 exons, which were examined pairwise to determine the overall nucleotide/exon identity between the four genes (Figure 7). Three major regions were delineated, each with varying degrees of sequence identity: Exons 2–13 comprised the extracellular segment (MAM, Ig and four fibronectin (FN) type III domains), exon 14–18 (juxtamembrane region), and exons 19–32 (two phosphatase domains). Although the number of exons comprising each of the extracellular domains was identical in each of the four genes, exon size varied in some domains and remained unchanged in others. Within the extracellular segment, the MAM domain showed the most extensive variation in exon size: The first exon ranged from 123 to 132 bp, and the third from 79 to 82bp (Figure 8). MAM domains are comprised of 160–170 amino acids containing four conserved cysteines; their function has been examined in some detail. When expressed in non-adherent cells, PTPμ [12-14] and PTPκ [15] proteins formed large calcium-independent clusters. Aggregation was strictly homophilic, consisting exclusively of cells expressing only a single R2B type [14-16]. Because this property had not been demonstrated with any of the other RPTP subfamilies, a crucial role for the MAM domain in this homophilic interaction was implied. However, in an in vitro binding assay in which regions of recombinant PTPμ were expressed [17], the homophilic binding site was localized to the immunoglobulin (Ig)-like domain. Subsequently, MAM and Ig domains were shown to function cooperatively in homophilic binding in both PTPμ and PTPκ [16]. It was suggested that the binding site is located in the Ig domain and the MAM domain is part of a "sorting" mechanism that confers homophilic binding specificity [6]. Figures 7 and 8 show that, when combined with the invariant 272 bp middle exon, each R2B MAM domain had a unique combination of exon sizes and low sequence identity, indicating a region of high specificity. The adjacent Ig-like domain contained exons of identical size, implying a less specific role than that of the MAM domain. These marked variations in sequence identity are consistent with the idea that the MAM domain plays a role in the mediation of homophilic binding specificity [6].

Bottom Line: The greatest variability in genomic organization and the majority of alternatively spliced exons were observed in the juxtamembrane domain, a region critical for the regulation of signal transduction.Comparison of the four R2B RPTP genes revealed virtually identical principles of genomic organization, despite great disparities in gene size due to variations in intron length.Although subtle differences in exon length were also observed, it is likely that functional differences among these genes arise from the specific combinations of exons generated by alternative splicing.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA. besco.1@osu.edu

ABSTRACT

Background: Four genes designated as PTPRK (PTPkappa), PTPRL/U (PCP-2), PTPRM (PTPmu) and PTPRT (PTPrho) code for a subfamily (type R2B) of receptor protein tyrosine phosphatases (RPTPs) uniquely characterized by the presence of an N-terminal MAM domain. These transmembrane molecules have been implicated in homophilic cell adhesion. In the human, the PTPRK gene is located on chromosome 6, PTPRL/U on 1, PTPRM on 18 and PTPRT on 20. In the mouse, the four genes ptprk, ptprl, ptprm and ptprt are located in syntenic regions of chromosomes 10, 4, 17 and 2, respectively.

Results: The genomic organization of murine R2B RPTP genes is described. The four genes varied greatly in size ranging from approximately 64 kb to approximately 1 Mb, primarily due to proportional differences in intron lengths. Although there were also minor variations in exon length, the number of exons and the phases of exon/intron junctions were highly conserved. In situ hybridization with digoxigenin-labeled cRNA probes was used to localize each of the four R2B transcripts to specific cell types within the murine central nervous system. Phylogenetic analysis of complete sequences indicated that PTPrho and PTPmu were most closely related, followed by PTPkappa. The most distant family member was PCP-2. Alignment of RPTP polypeptide sequences predicted putative alternatively spliced exons. PCR experiments revealed that five of these exons were alternatively spliced, and that each of the four phosphatases incorporated them differently. The greatest variability in genomic organization and the majority of alternatively spliced exons were observed in the juxtamembrane domain, a region critical for the regulation of signal transduction.

Conclusions: Comparison of the four R2B RPTP genes revealed virtually identical principles of genomic organization, despite great disparities in gene size due to variations in intron length. Although subtle differences in exon length were also observed, it is likely that functional differences among these genes arise from the specific combinations of exons generated by alternative splicing.

Show MeSH
Related in: MedlinePlus