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Identification of three prominin homologs and characterization of their messenger RNA expression in Xenopus laevis tissues.

Han Z, Papermaster DS - Mol. Vis. (2011)

Bottom Line: Two of these homologs are likely to be the X. laevis orthologs of mammalian prominin-1 and 2, respectively, while the third homolog is likely to be the X. laevis ortholog of prominin-3, which was only found in nonmammalian vertebrates and the platypus.Similar to mammalian prominin-1, we found that exons 26b, 27, and 28a of the X. laevis prominin-1 gene are alternatively spliced, and that the splice isoforms of mRNA show tissue-specific expression profiles.Our results suggest that the mRNAs of prominin homologs are expressed in many tissues of X. laevis, but differ in their expression levels and mRNA splicing.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030, USA.

ABSTRACT

Purpose: Prominin is a family of pentaspan transmembrane glycoproteins. They are expressed in various types of cells, including many stem/progenitor cells. Prominin-1 plays an important role in generating and maintaining the structure of the photoreceptors. In this study, we identified three prominin homologs in Xenopus laevis, a model animal widely used in vision research, and characterized their messenger RNA (mRNA) expression in selected tissues of this frog.

Methods: Reverse-transcription PCR (RT-PCR) and rapid amplification of cDNA ends (RACE) were used to isolate cDNAs of prominin homologs. Semiquantitative RT-PCR was used to measure the relative expression levels of mRNAs of the three prominin homologs in four X. laevis tissues, specifically those of the retina, brain, testis, and kidney. Sequences of prominin homologs were analyzed with bioinformatic software.

Results: We isolated cDNAs of three prominin homologs from X. laevis tissues and compared their sequences with previously described prominin-1, 2, and 3 sequences from other species using phylogenetic analysis. Two of these homologs are likely to be the X. laevis orthologs of mammalian prominin-1 and 2, respectively, while the third homolog is likely to be the X. laevis ortholog of prominin-3, which was only found in nonmammalian vertebrates and the platypus. We identified alternatively spliced exons in mRNAs of all three prominin homologs. Similar to mammalian prominin-1, we found that exons 26b, 27, and 28a of the X. laevis prominin-1 gene are alternatively spliced, and that the splice isoforms of mRNA show tissue-specific expression profiles. We found that prominin-1 was the most abundant homolog expressed in the retina, brain, and testis, while prominin-3 was the most abundant homolog in the kidney. The expression level of prominin-2 was the lowest of the three prominin homologs in all four examined tissues of this frog.

Conclusions: Our results suggest that the mRNAs of prominin homologs are expressed in many tissues of X. laevis, but differ in their expression levels and mRNA splicing. Prominin-1 is the most abundant of the three prominin homologs expressed in the frog retina.

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Comparison of exon organization of prominin-1 gene from X. laevis, mouse, and human. It appears that the gene structure of prominin-1 is evolutionarily conserved in these animals. Alternative splicing of the prominin-1 gene is seen in all three animals, however, with considerable differences in the choices of alternative exons and the splicing patterns. Homologous exons of xlProminin-1 and mouse and human prominin-1 are aligned for comparison of their exon organization. Constitutive exons are marked in black. Alternatively spliced exons are marked in orange. Spliced forms identified in cDNA clones are indicated by jointed lines. Note that homologous exons are assigned with the same number to maintain consistency with preexisting nomenclature [2,31]. Exons 26b and 27 are conserved and alternatively spliced in all three species. Alternative exons 3a, 8a, 11a, and 28a of xlProminin-1 are not found in mouse or human prominin-1. Splicing of alternative exons 4a results from using an alternative 3′ splice site in exon 4, and is only observed in mouse prominin-1 [31]. Alternative exon 19 of xlProminin-1 is alternatively spliced in mouse prominin-1, but no evidence has been found that this exon is alternatively spliced in human prominin-1. Alternative exon 25 of human prominin-1 is not found in prominin-1 from the mouse or X. laevis. The alternative exon 26a of mouse prominin-1 and the alternative exons 25 and 26a of human prominin-1 are not found in xlProminin-1. Exons 3, 9, and 28 of mouse prominin-1 are alternative, but appear to be constitutive in X. laevis. The region encompassing exons 24 to 28 of xlProminin-1 and homologous sequences of the prominin-1 gene from the mouse and human are regions of extensive alternative splicing. Diagrams of translated proteins are aligned with their coding sequences. Divisions of proteins by predicted transmembrane domains are marked.
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f6: Comparison of exon organization of prominin-1 gene from X. laevis, mouse, and human. It appears that the gene structure of prominin-1 is evolutionarily conserved in these animals. Alternative splicing of the prominin-1 gene is seen in all three animals, however, with considerable differences in the choices of alternative exons and the splicing patterns. Homologous exons of xlProminin-1 and mouse and human prominin-1 are aligned for comparison of their exon organization. Constitutive exons are marked in black. Alternatively spliced exons are marked in orange. Spliced forms identified in cDNA clones are indicated by jointed lines. Note that homologous exons are assigned with the same number to maintain consistency with preexisting nomenclature [2,31]. Exons 26b and 27 are conserved and alternatively spliced in all three species. Alternative exons 3a, 8a, 11a, and 28a of xlProminin-1 are not found in mouse or human prominin-1. Splicing of alternative exons 4a results from using an alternative 3′ splice site in exon 4, and is only observed in mouse prominin-1 [31]. Alternative exon 19 of xlProminin-1 is alternatively spliced in mouse prominin-1, but no evidence has been found that this exon is alternatively spliced in human prominin-1. Alternative exon 25 of human prominin-1 is not found in prominin-1 from the mouse or X. laevis. The alternative exon 26a of mouse prominin-1 and the alternative exons 25 and 26a of human prominin-1 are not found in xlProminin-1. Exons 3, 9, and 28 of mouse prominin-1 are alternative, but appear to be constitutive in X. laevis. The region encompassing exons 24 to 28 of xlProminin-1 and homologous sequences of the prominin-1 gene from the mouse and human are regions of extensive alternative splicing. Diagrams of translated proteins are aligned with their coding sequences. Divisions of proteins by predicted transmembrane domains are marked.

Mentions: The organization and splicing of prominin-1 exons in the mouse and human have been well characterized [30-32]. To determine whether the gene structure is conserved in xlProminin-1, we aligned all identified exons of prominin-1 from X. laevis, mice, and humans (Figure 6). Some exons found in one species were absent in another, but these were always alternatively spliced exons (Figure 6). We also correlated the positions of all alternatively spliced exons of xlProminin-1 to its membrane topology and found that all alternatively spliced exons represent sequences coding for the extracellular domains (E1, E2, and E3) or the C-terminus of the protein, as was previously observed in prominin-1 from mouse and human [3,30-32].


Identification of three prominin homologs and characterization of their messenger RNA expression in Xenopus laevis tissues.

Han Z, Papermaster DS - Mol. Vis. (2011)

Comparison of exon organization of prominin-1 gene from X. laevis, mouse, and human. It appears that the gene structure of prominin-1 is evolutionarily conserved in these animals. Alternative splicing of the prominin-1 gene is seen in all three animals, however, with considerable differences in the choices of alternative exons and the splicing patterns. Homologous exons of xlProminin-1 and mouse and human prominin-1 are aligned for comparison of their exon organization. Constitutive exons are marked in black. Alternatively spliced exons are marked in orange. Spliced forms identified in cDNA clones are indicated by jointed lines. Note that homologous exons are assigned with the same number to maintain consistency with preexisting nomenclature [2,31]. Exons 26b and 27 are conserved and alternatively spliced in all three species. Alternative exons 3a, 8a, 11a, and 28a of xlProminin-1 are not found in mouse or human prominin-1. Splicing of alternative exons 4a results from using an alternative 3′ splice site in exon 4, and is only observed in mouse prominin-1 [31]. Alternative exon 19 of xlProminin-1 is alternatively spliced in mouse prominin-1, but no evidence has been found that this exon is alternatively spliced in human prominin-1. Alternative exon 25 of human prominin-1 is not found in prominin-1 from the mouse or X. laevis. The alternative exon 26a of mouse prominin-1 and the alternative exons 25 and 26a of human prominin-1 are not found in xlProminin-1. Exons 3, 9, and 28 of mouse prominin-1 are alternative, but appear to be constitutive in X. laevis. The region encompassing exons 24 to 28 of xlProminin-1 and homologous sequences of the prominin-1 gene from the mouse and human are regions of extensive alternative splicing. Diagrams of translated proteins are aligned with their coding sequences. Divisions of proteins by predicted transmembrane domains are marked.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3108902&req=5

f6: Comparison of exon organization of prominin-1 gene from X. laevis, mouse, and human. It appears that the gene structure of prominin-1 is evolutionarily conserved in these animals. Alternative splicing of the prominin-1 gene is seen in all three animals, however, with considerable differences in the choices of alternative exons and the splicing patterns. Homologous exons of xlProminin-1 and mouse and human prominin-1 are aligned for comparison of their exon organization. Constitutive exons are marked in black. Alternatively spliced exons are marked in orange. Spliced forms identified in cDNA clones are indicated by jointed lines. Note that homologous exons are assigned with the same number to maintain consistency with preexisting nomenclature [2,31]. Exons 26b and 27 are conserved and alternatively spliced in all three species. Alternative exons 3a, 8a, 11a, and 28a of xlProminin-1 are not found in mouse or human prominin-1. Splicing of alternative exons 4a results from using an alternative 3′ splice site in exon 4, and is only observed in mouse prominin-1 [31]. Alternative exon 19 of xlProminin-1 is alternatively spliced in mouse prominin-1, but no evidence has been found that this exon is alternatively spliced in human prominin-1. Alternative exon 25 of human prominin-1 is not found in prominin-1 from the mouse or X. laevis. The alternative exon 26a of mouse prominin-1 and the alternative exons 25 and 26a of human prominin-1 are not found in xlProminin-1. Exons 3, 9, and 28 of mouse prominin-1 are alternative, but appear to be constitutive in X. laevis. The region encompassing exons 24 to 28 of xlProminin-1 and homologous sequences of the prominin-1 gene from the mouse and human are regions of extensive alternative splicing. Diagrams of translated proteins are aligned with their coding sequences. Divisions of proteins by predicted transmembrane domains are marked.
Mentions: The organization and splicing of prominin-1 exons in the mouse and human have been well characterized [30-32]. To determine whether the gene structure is conserved in xlProminin-1, we aligned all identified exons of prominin-1 from X. laevis, mice, and humans (Figure 6). Some exons found in one species were absent in another, but these were always alternatively spliced exons (Figure 6). We also correlated the positions of all alternatively spliced exons of xlProminin-1 to its membrane topology and found that all alternatively spliced exons represent sequences coding for the extracellular domains (E1, E2, and E3) or the C-terminus of the protein, as was previously observed in prominin-1 from mouse and human [3,30-32].

Bottom Line: Two of these homologs are likely to be the X. laevis orthologs of mammalian prominin-1 and 2, respectively, while the third homolog is likely to be the X. laevis ortholog of prominin-3, which was only found in nonmammalian vertebrates and the platypus.Similar to mammalian prominin-1, we found that exons 26b, 27, and 28a of the X. laevis prominin-1 gene are alternatively spliced, and that the splice isoforms of mRNA show tissue-specific expression profiles.Our results suggest that the mRNAs of prominin homologs are expressed in many tissues of X. laevis, but differ in their expression levels and mRNA splicing.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030, USA.

ABSTRACT

Purpose: Prominin is a family of pentaspan transmembrane glycoproteins. They are expressed in various types of cells, including many stem/progenitor cells. Prominin-1 plays an important role in generating and maintaining the structure of the photoreceptors. In this study, we identified three prominin homologs in Xenopus laevis, a model animal widely used in vision research, and characterized their messenger RNA (mRNA) expression in selected tissues of this frog.

Methods: Reverse-transcription PCR (RT-PCR) and rapid amplification of cDNA ends (RACE) were used to isolate cDNAs of prominin homologs. Semiquantitative RT-PCR was used to measure the relative expression levels of mRNAs of the three prominin homologs in four X. laevis tissues, specifically those of the retina, brain, testis, and kidney. Sequences of prominin homologs were analyzed with bioinformatic software.

Results: We isolated cDNAs of three prominin homologs from X. laevis tissues and compared their sequences with previously described prominin-1, 2, and 3 sequences from other species using phylogenetic analysis. Two of these homologs are likely to be the X. laevis orthologs of mammalian prominin-1 and 2, respectively, while the third homolog is likely to be the X. laevis ortholog of prominin-3, which was only found in nonmammalian vertebrates and the platypus. We identified alternatively spliced exons in mRNAs of all three prominin homologs. Similar to mammalian prominin-1, we found that exons 26b, 27, and 28a of the X. laevis prominin-1 gene are alternatively spliced, and that the splice isoforms of mRNA show tissue-specific expression profiles. We found that prominin-1 was the most abundant homolog expressed in the retina, brain, and testis, while prominin-3 was the most abundant homolog in the kidney. The expression level of prominin-2 was the lowest of the three prominin homologs in all four examined tissues of this frog.

Conclusions: Our results suggest that the mRNAs of prominin homologs are expressed in many tissues of X. laevis, but differ in their expression levels and mRNA splicing. Prominin-1 is the most abundant of the three prominin homologs expressed in the frog retina.

Show MeSH
Related in: MedlinePlus