Limits...
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.

Show MeSH

Related in: MedlinePlus

Phylogenic analysis of prominin homologs from several species. This phylogenetic tree was constructed to show the existence of multiple prominin homologs in metazoan animals from fly to human and their evolutionary relationship. Three X. laevis prominin homologs, designated as xlProminin-1, 2, and 3, are placed in branches of the consensus phylogenetic tree with prominin-1, 2, and 3 from other species. The numbers at each node are the percentage bootstrapping values of 100 replicates. The evolutionary distance of any two sequences is represented by the length of the branches. Sequences used in the phylogenetic analysis are excerpted from: H. sapien Prom-1 (NP_006008), P. troglodytes Prom-1 (XP_517115), M. mulatta Prom-1 (NP_001070888), R. norvegicus Prom-1 (NP_068519), M. musculus Prom-1 (NP_032961), C. familiaris Prom-1 (XP_850831), B. taurus Prom-1 (HQ159409), E. caballus Prom-1 (XM_001498729), D. rerio Prom-1a (NP_001108615), T. rubripes Prom-1a (HQ159405), D. rerio Prom-1b (NP_932337), T. rubripes Prom-1b (HQ159406), O. anatinus Prom-1 (HQ159408), G. gallus Prom-1 (XP_001232165), X. laevis Prom-1 (XM_001163920), X. tropicalis Prom-1 (HQ159400), H. sapien Prom-2 (NP_653308), P. troglodytes Prom-2 (XP_001143498), C. familiaris Prom-2 (XP_854455), B. taurus Prom-2 (XP_599188), E. caballus Prom-2 (XP_001494215), R. norvegicus Prom-2 (AAN63818), M. musculus Prom-2 (NP_620089), X. laevis Prom-2 (NP_001163922), X. tropicalis Prom-2 (HQ159402), X. laevis Prom-3 (NP_001163921), X. tropicalis Prom-3 (HQ159403), D. rerio Prom-3 (XP_684527), T. rubripes Prom-3 (HQ159407), D. melanogaster Prominin (ABH07113), D. melanogaster Prominin-like protein AF127935 (NP_647770), C. elegans protein F08B12 (NP_509907), C. elegans protein M28.8 (NP_496294), C. elegans protein M28.9 (NP_496296).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3108902&req=5

f2: Phylogenic analysis of prominin homologs from several species. This phylogenetic tree was constructed to show the existence of multiple prominin homologs in metazoan animals from fly to human and their evolutionary relationship. Three X. laevis prominin homologs, designated as xlProminin-1, 2, and 3, are placed in branches of the consensus phylogenetic tree with prominin-1, 2, and 3 from other species. The numbers at each node are the percentage bootstrapping values of 100 replicates. The evolutionary distance of any two sequences is represented by the length of the branches. Sequences used in the phylogenetic analysis are excerpted from: H. sapien Prom-1 (NP_006008), P. troglodytes Prom-1 (XP_517115), M. mulatta Prom-1 (NP_001070888), R. norvegicus Prom-1 (NP_068519), M. musculus Prom-1 (NP_032961), C. familiaris Prom-1 (XP_850831), B. taurus Prom-1 (HQ159409), E. caballus Prom-1 (XM_001498729), D. rerio Prom-1a (NP_001108615), T. rubripes Prom-1a (HQ159405), D. rerio Prom-1b (NP_932337), T. rubripes Prom-1b (HQ159406), O. anatinus Prom-1 (HQ159408), G. gallus Prom-1 (XP_001232165), X. laevis Prom-1 (XM_001163920), X. tropicalis Prom-1 (HQ159400), H. sapien Prom-2 (NP_653308), P. troglodytes Prom-2 (XP_001143498), C. familiaris Prom-2 (XP_854455), B. taurus Prom-2 (XP_599188), E. caballus Prom-2 (XP_001494215), R. norvegicus Prom-2 (AAN63818), M. musculus Prom-2 (NP_620089), X. laevis Prom-2 (NP_001163922), X. tropicalis Prom-2 (HQ159402), X. laevis Prom-3 (NP_001163921), X. tropicalis Prom-3 (HQ159403), D. rerio Prom-3 (XP_684527), T. rubripes Prom-3 (HQ159407), D. melanogaster Prominin (ABH07113), D. melanogaster Prominin-like protein AF127935 (NP_647770), C. elegans protein F08B12 (NP_509907), C. elegans protein M28.8 (NP_496294), C. elegans protein M28.9 (NP_496296).

Mentions: Previous taxonomic studies of prominins have divided prominin homologs into three groups. These are prominin-1 [2,31] and prominin-2 in mammals [3], and prominin-3 in zebrafish [52]. Two variants of prominin-1, namely prominin-1a and 1b, were identified in zebrafish [52]. We performed protein phylogenetic analysis using the PhyML 3.0 software to compare X. laevis prominin homologs with available prominin sequences; the results are presented in Figure 2. The sequences used to construct the phylogenetic tree were from online public databases, newly cloned cDNAs, or predicted mRNAs from genomic sequences (Methods). Since the N- and C-termini of prominin homologs were incomplete in many of the retrieved sequences, only the sequences from exon 4 to exon 24 of prominin-1 and homologous sequences of other prominins were used for the phylogenetic analysis. The analysis revealed that the first cloned prominin homolog is the X. laevis ortholog of prominin-1, and is therefore designated as xlProminin-1. The other two prominin-like cDNAs found in X. laevis were named xlProminin-2 and xlProminin-3 according to their positions on the phylogenetic tree.


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

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

Phylogenic analysis of prominin homologs from several species. This phylogenetic tree was constructed to show the existence of multiple prominin homologs in metazoan animals from fly to human and their evolutionary relationship. Three X. laevis prominin homologs, designated as xlProminin-1, 2, and 3, are placed in branches of the consensus phylogenetic tree with prominin-1, 2, and 3 from other species. The numbers at each node are the percentage bootstrapping values of 100 replicates. The evolutionary distance of any two sequences is represented by the length of the branches. Sequences used in the phylogenetic analysis are excerpted from: H. sapien Prom-1 (NP_006008), P. troglodytes Prom-1 (XP_517115), M. mulatta Prom-1 (NP_001070888), R. norvegicus Prom-1 (NP_068519), M. musculus Prom-1 (NP_032961), C. familiaris Prom-1 (XP_850831), B. taurus Prom-1 (HQ159409), E. caballus Prom-1 (XM_001498729), D. rerio Prom-1a (NP_001108615), T. rubripes Prom-1a (HQ159405), D. rerio Prom-1b (NP_932337), T. rubripes Prom-1b (HQ159406), O. anatinus Prom-1 (HQ159408), G. gallus Prom-1 (XP_001232165), X. laevis Prom-1 (XM_001163920), X. tropicalis Prom-1 (HQ159400), H. sapien Prom-2 (NP_653308), P. troglodytes Prom-2 (XP_001143498), C. familiaris Prom-2 (XP_854455), B. taurus Prom-2 (XP_599188), E. caballus Prom-2 (XP_001494215), R. norvegicus Prom-2 (AAN63818), M. musculus Prom-2 (NP_620089), X. laevis Prom-2 (NP_001163922), X. tropicalis Prom-2 (HQ159402), X. laevis Prom-3 (NP_001163921), X. tropicalis Prom-3 (HQ159403), D. rerio Prom-3 (XP_684527), T. rubripes Prom-3 (HQ159407), D. melanogaster Prominin (ABH07113), D. melanogaster Prominin-like protein AF127935 (NP_647770), C. elegans protein F08B12 (NP_509907), C. elegans protein M28.8 (NP_496294), C. elegans protein M28.9 (NP_496296).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Phylogenic analysis of prominin homologs from several species. This phylogenetic tree was constructed to show the existence of multiple prominin homologs in metazoan animals from fly to human and their evolutionary relationship. Three X. laevis prominin homologs, designated as xlProminin-1, 2, and 3, are placed in branches of the consensus phylogenetic tree with prominin-1, 2, and 3 from other species. The numbers at each node are the percentage bootstrapping values of 100 replicates. The evolutionary distance of any two sequences is represented by the length of the branches. Sequences used in the phylogenetic analysis are excerpted from: H. sapien Prom-1 (NP_006008), P. troglodytes Prom-1 (XP_517115), M. mulatta Prom-1 (NP_001070888), R. norvegicus Prom-1 (NP_068519), M. musculus Prom-1 (NP_032961), C. familiaris Prom-1 (XP_850831), B. taurus Prom-1 (HQ159409), E. caballus Prom-1 (XM_001498729), D. rerio Prom-1a (NP_001108615), T. rubripes Prom-1a (HQ159405), D. rerio Prom-1b (NP_932337), T. rubripes Prom-1b (HQ159406), O. anatinus Prom-1 (HQ159408), G. gallus Prom-1 (XP_001232165), X. laevis Prom-1 (XM_001163920), X. tropicalis Prom-1 (HQ159400), H. sapien Prom-2 (NP_653308), P. troglodytes Prom-2 (XP_001143498), C. familiaris Prom-2 (XP_854455), B. taurus Prom-2 (XP_599188), E. caballus Prom-2 (XP_001494215), R. norvegicus Prom-2 (AAN63818), M. musculus Prom-2 (NP_620089), X. laevis Prom-2 (NP_001163922), X. tropicalis Prom-2 (HQ159402), X. laevis Prom-3 (NP_001163921), X. tropicalis Prom-3 (HQ159403), D. rerio Prom-3 (XP_684527), T. rubripes Prom-3 (HQ159407), D. melanogaster Prominin (ABH07113), D. melanogaster Prominin-like protein AF127935 (NP_647770), C. elegans protein F08B12 (NP_509907), C. elegans protein M28.8 (NP_496294), C. elegans protein M28.9 (NP_496296).
Mentions: Previous taxonomic studies of prominins have divided prominin homologs into three groups. These are prominin-1 [2,31] and prominin-2 in mammals [3], and prominin-3 in zebrafish [52]. Two variants of prominin-1, namely prominin-1a and 1b, were identified in zebrafish [52]. We performed protein phylogenetic analysis using the PhyML 3.0 software to compare X. laevis prominin homologs with available prominin sequences; the results are presented in Figure 2. The sequences used to construct the phylogenetic tree were from online public databases, newly cloned cDNAs, or predicted mRNAs from genomic sequences (Methods). Since the N- and C-termini of prominin homologs were incomplete in many of the retrieved sequences, only the sequences from exon 4 to exon 24 of prominin-1 and homologous sequences of other prominins were used for the phylogenetic analysis. The analysis revealed that the first cloned prominin homolog is the X. laevis ortholog of prominin-1, and is therefore designated as xlProminin-1. The other two prominin-like cDNAs found in X. laevis were named xlProminin-2 and xlProminin-3 according to their positions on the phylogenetic tree.

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