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Comparative genomic analysis of slc39a12/ZIP12: insight into a zinc transporter required for vertebrate nervous system development.

Chowanadisai W - PLoS ONE (2014)

Bottom Line: The hypothesis that ZIP12 is a zinc transporter important for nervous system function and development guided a comparative genetics approach to uncover the presence of ZIP12 in various genomes and identify conserved sequences and expression patterns associated with ZIP12.The discrimination of ZIP12 compared to ZIP4 was unsuccessful or inconclusive in other invertebrate chordates and deuterostomes.Consequently, the role of ZIP12 may be an important link to reported congenital malformations in numerous animal models and humans that are caused by zinc deficiency.

View Article: PubMed Central - PubMed

Affiliation: Department of Nutrition, University of California Davis, Davis, California, United States of America.

ABSTRACT
The zinc transporter ZIP12, which is encoded by the gene slc39a12, has previously been shown to be important for neuronal differentiation in mouse Neuro-2a neuroblastoma cells and primary mouse neurons and necessary for neurulation during Xenopus tropicalis embryogenesis. However, relatively little is known about the biochemical properties, cellular regulation, or the physiological role of this gene. The hypothesis that ZIP12 is a zinc transporter important for nervous system function and development guided a comparative genetics approach to uncover the presence of ZIP12 in various genomes and identify conserved sequences and expression patterns associated with ZIP12. Ortholog detection of slc39a12 was conducted with reciprocal BLAST hits with the amino acid sequence of human ZIP12 in comparison to the human paralog ZIP4 and conserved local synteny between genomes. ZIP12 is present in the genomes of almost all vertebrates examined, from humans and other mammals to most teleost fish. However, ZIP12 appears to be absent from the zebrafish genome. The discrimination of ZIP12 compared to ZIP4 was unsuccessful or inconclusive in other invertebrate chordates and deuterostomes. Splice variation, due to the inclusion or exclusion of a conserved exon, is present in humans, rats, and cows and likely has biological significance. ZIP12 also possesses many putative di-leucine and tyrosine motifs often associated with intracellular trafficking, which may control cellular zinc uptake activity through the localization of ZIP12 within the cell. These findings highlight multiple aspects of ZIP12 at the biochemical, cellular, and physiological levels with likely biological significance. ZIP12 appears to have conserved function as a zinc uptake transporter in vertebrate nervous system development. Consequently, the role of ZIP12 may be an important link to reported congenital malformations in numerous animal models and humans that are caused by zinc deficiency.

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Histidine-rich exon 9 present in human and mouse ZIP12 is also present in cow, opossum, and chicken genomes.Organism common names are accompanied by accession numbers, corresponding nucleotides, and translated amino acid sequence. Amino acids conserved between humans and mice are shaded in black. Corresponding amino acids that are conserved in cow, opossum, and chicken are shaded in grey.
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pone-0111535-g007: Histidine-rich exon 9 present in human and mouse ZIP12 is also present in cow, opossum, and chicken genomes.Organism common names are accompanied by accession numbers, corresponding nucleotides, and translated amino acid sequence. Amino acids conserved between humans and mice are shaded in black. Corresponding amino acids that are conserved in cow, opossum, and chicken are shaded in grey.

Mentions: The alignment (Figure S3) uncovered 2 different isoforms of ZIP12 frequently detected across many species which correspond to the inclusion or exclusion of exon 9. Furthermore, this exon was present in at least two non-mammalian organisms, Xenopus tropicalis and tilapia (Figure S1), which supports an ancestral history for this exon in slc39a12 that precedes the split with birds and mammals [82]. Although this exon is likely present in other mammalian organisms, the longer isoform has not been described previously in chicken, cow, opossum, or platypus. TBLASTN searches for exon 9 showed that the sequence is present in cow, chicken, and opossum genomes (Figure 7). This sequence was not detected in the platypus, but this may be due to gaps in the genomic sequence [GenBank: NW_001594582, 1525899-1525899, 1527878-1528642]. Reverse transcriptase-polymerase chain reaction (RT-PCR) was used to determine that both isoforms are expressed in humans, cows, and rats (Figure 8A-8C). However, the shorter isoform in mice (Figure 8D) could not be detected by RT-PCR despite repeated attempts with different primer sequences and PCR cycling conditions (data not shown). The reading frame in this exon appears to be conserved across species (111 bp in humans and 108 bp in other species, Figure 9). It is possible that the reading frame of this exon is conserved, so that inclusion or exclusion of this exon does not affect the downstream reading frame. The translated product of this exon is expected to increase the length of a cytoplasmic loop between transmembrane domains 3 and 4 of ZIP12 [21]. The transcript variation of ZIP12 is likely due to exon skipping, which is the most common form of splice variation [83]. The intron-exon structure flanking exon 9 is conserved across multiple vertebrate and mammalian species (Figure 2), which supports the notion that this variation has biological significance. Because this region of ZIP12 encodes a histidine-rich segment that is expected to lengthen a cytoplasmic loop [21], [48], this region could be important for post-translational regulation of ZIP12. In support of this possible function, ZIP4 contains a similarly located histidine-rich, cytoplasmic-facing motif that is sensitive to zinc and required for ubiquitin-mediated protein degradation in response to excess zinc [47]. Wide-scale global approaches have used comparative genomics to discover novel human exons that were previously unidentified because of weak or lacking cDNA support due to low transcript levels or restricted tissue specificity [84].


Comparative genomic analysis of slc39a12/ZIP12: insight into a zinc transporter required for vertebrate nervous system development.

Chowanadisai W - PLoS ONE (2014)

Histidine-rich exon 9 present in human and mouse ZIP12 is also present in cow, opossum, and chicken genomes.Organism common names are accompanied by accession numbers, corresponding nucleotides, and translated amino acid sequence. Amino acids conserved between humans and mice are shaded in black. Corresponding amino acids that are conserved in cow, opossum, and chicken are shaded in grey.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222902&req=5

pone-0111535-g007: Histidine-rich exon 9 present in human and mouse ZIP12 is also present in cow, opossum, and chicken genomes.Organism common names are accompanied by accession numbers, corresponding nucleotides, and translated amino acid sequence. Amino acids conserved between humans and mice are shaded in black. Corresponding amino acids that are conserved in cow, opossum, and chicken are shaded in grey.
Mentions: The alignment (Figure S3) uncovered 2 different isoforms of ZIP12 frequently detected across many species which correspond to the inclusion or exclusion of exon 9. Furthermore, this exon was present in at least two non-mammalian organisms, Xenopus tropicalis and tilapia (Figure S1), which supports an ancestral history for this exon in slc39a12 that precedes the split with birds and mammals [82]. Although this exon is likely present in other mammalian organisms, the longer isoform has not been described previously in chicken, cow, opossum, or platypus. TBLASTN searches for exon 9 showed that the sequence is present in cow, chicken, and opossum genomes (Figure 7). This sequence was not detected in the platypus, but this may be due to gaps in the genomic sequence [GenBank: NW_001594582, 1525899-1525899, 1527878-1528642]. Reverse transcriptase-polymerase chain reaction (RT-PCR) was used to determine that both isoforms are expressed in humans, cows, and rats (Figure 8A-8C). However, the shorter isoform in mice (Figure 8D) could not be detected by RT-PCR despite repeated attempts with different primer sequences and PCR cycling conditions (data not shown). The reading frame in this exon appears to be conserved across species (111 bp in humans and 108 bp in other species, Figure 9). It is possible that the reading frame of this exon is conserved, so that inclusion or exclusion of this exon does not affect the downstream reading frame. The translated product of this exon is expected to increase the length of a cytoplasmic loop between transmembrane domains 3 and 4 of ZIP12 [21]. The transcript variation of ZIP12 is likely due to exon skipping, which is the most common form of splice variation [83]. The intron-exon structure flanking exon 9 is conserved across multiple vertebrate and mammalian species (Figure 2), which supports the notion that this variation has biological significance. Because this region of ZIP12 encodes a histidine-rich segment that is expected to lengthen a cytoplasmic loop [21], [48], this region could be important for post-translational regulation of ZIP12. In support of this possible function, ZIP4 contains a similarly located histidine-rich, cytoplasmic-facing motif that is sensitive to zinc and required for ubiquitin-mediated protein degradation in response to excess zinc [47]. Wide-scale global approaches have used comparative genomics to discover novel human exons that were previously unidentified because of weak or lacking cDNA support due to low transcript levels or restricted tissue specificity [84].

Bottom Line: The hypothesis that ZIP12 is a zinc transporter important for nervous system function and development guided a comparative genetics approach to uncover the presence of ZIP12 in various genomes and identify conserved sequences and expression patterns associated with ZIP12.The discrimination of ZIP12 compared to ZIP4 was unsuccessful or inconclusive in other invertebrate chordates and deuterostomes.Consequently, the role of ZIP12 may be an important link to reported congenital malformations in numerous animal models and humans that are caused by zinc deficiency.

View Article: PubMed Central - PubMed

Affiliation: Department of Nutrition, University of California Davis, Davis, California, United States of America.

ABSTRACT
The zinc transporter ZIP12, which is encoded by the gene slc39a12, has previously been shown to be important for neuronal differentiation in mouse Neuro-2a neuroblastoma cells and primary mouse neurons and necessary for neurulation during Xenopus tropicalis embryogenesis. However, relatively little is known about the biochemical properties, cellular regulation, or the physiological role of this gene. The hypothesis that ZIP12 is a zinc transporter important for nervous system function and development guided a comparative genetics approach to uncover the presence of ZIP12 in various genomes and identify conserved sequences and expression patterns associated with ZIP12. Ortholog detection of slc39a12 was conducted with reciprocal BLAST hits with the amino acid sequence of human ZIP12 in comparison to the human paralog ZIP4 and conserved local synteny between genomes. ZIP12 is present in the genomes of almost all vertebrates examined, from humans and other mammals to most teleost fish. However, ZIP12 appears to be absent from the zebrafish genome. The discrimination of ZIP12 compared to ZIP4 was unsuccessful or inconclusive in other invertebrate chordates and deuterostomes. Splice variation, due to the inclusion or exclusion of a conserved exon, is present in humans, rats, and cows and likely has biological significance. ZIP12 also possesses many putative di-leucine and tyrosine motifs often associated with intracellular trafficking, which may control cellular zinc uptake activity through the localization of ZIP12 within the cell. These findings highlight multiple aspects of ZIP12 at the biochemical, cellular, and physiological levels with likely biological significance. ZIP12 appears to have conserved function as a zinc uptake transporter in vertebrate nervous system development. Consequently, the role of ZIP12 may be an important link to reported congenital malformations in numerous animal models and humans that are caused by zinc deficiency.

Show MeSH
Related in: MedlinePlus