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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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Related in: MedlinePlus

Alignment for 5′ UTR, first 90 bp of coding region, and the proximal promoter (1000 bp upstream of transcription start site) of human, mouse, and cow slc39a12.Lowercase and uppercase in sequences indicate nucleotide and amino acid sequences, respectively. Black shaded text indicates possible transcription factor binding sites in largely conserved regions. Gray shaded text indicates 5′ UTR. For coding regions, possible signal peptide is underlined. Asterisks indicate nucleotides conserved in all sequences following alignment.
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pone-0111535-g005: Alignment for 5′ UTR, first 90 bp of coding region, and the proximal promoter (1000 bp upstream of transcription start site) of human, mouse, and cow slc39a12.Lowercase and uppercase in sequences indicate nucleotide and amino acid sequences, respectively. Black shaded text indicates possible transcription factor binding sites in largely conserved regions. Gray shaded text indicates 5′ UTR. For coding regions, possible signal peptide is underlined. Asterisks indicate nucleotides conserved in all sequences following alignment.

Mentions: Many of the predicted sequences for slc39a12 (Table 1) were performed through computational analyses [30], and some sequences lack biological evidence such as cDNA support. Bioinformatic and computational analyses are extremely useful, especially for genome-wide annotation of genes, but there can be some discrepancies or unresolved regions [74]. Accordingly, some differences were detected between annotated versions of slc39a12 solely derived from computation and other versions of slc39a12 with additional bases including expressed sequence tags (ESTs) and other biological experimentation. Comparisons with other ZIP12 sequences showed that the rat ZIP12 protein sequence [GenBank: NP_001099594] was likely missing the N-terminus (Figure S3). As a result, the N-terminus of ZIP12 in this report was reconstituted from the translated sequences of a rat EST [GenBank: FM065041] and 12 nucleotides of the rat genome [GenBank: NW_047496 3955687-3955698] (Figure 4, Figure S3). The 5′ untranslated region (UTR) of the annotated cow ZIP12 [GenBank: NM_001076878] (Figure 5) is missing at least 60 bp, based upon EST data and the observation that the conserved exon-intron structure of human, mouse, and chicken slc39a12 has the start codon in exon 2 (Figure 1, Figure 2). A comparison of the 5′ end of 2 EST clones [GenBank: EV626550 and EE901356] aligns to a separate exon in the cow genome [GenBank: AC_000170, 32666526-32666609]. The refinement of draft genome sequences and the correct annotation of gene sequences is important because genome sequences often provide the initial foundation for biological experimentation, particularly in reverse genetics.


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

Chowanadisai W - PLoS ONE (2014)

Alignment for 5′ UTR, first 90 bp of coding region, and the proximal promoter (1000 bp upstream of transcription start site) of human, mouse, and cow slc39a12.Lowercase and uppercase in sequences indicate nucleotide and amino acid sequences, respectively. Black shaded text indicates possible transcription factor binding sites in largely conserved regions. Gray shaded text indicates 5′ UTR. For coding regions, possible signal peptide is underlined. Asterisks indicate nucleotides conserved in all sequences following alignment.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111535-g005: Alignment for 5′ UTR, first 90 bp of coding region, and the proximal promoter (1000 bp upstream of transcription start site) of human, mouse, and cow slc39a12.Lowercase and uppercase in sequences indicate nucleotide and amino acid sequences, respectively. Black shaded text indicates possible transcription factor binding sites in largely conserved regions. Gray shaded text indicates 5′ UTR. For coding regions, possible signal peptide is underlined. Asterisks indicate nucleotides conserved in all sequences following alignment.
Mentions: Many of the predicted sequences for slc39a12 (Table 1) were performed through computational analyses [30], and some sequences lack biological evidence such as cDNA support. Bioinformatic and computational analyses are extremely useful, especially for genome-wide annotation of genes, but there can be some discrepancies or unresolved regions [74]. Accordingly, some differences were detected between annotated versions of slc39a12 solely derived from computation and other versions of slc39a12 with additional bases including expressed sequence tags (ESTs) and other biological experimentation. Comparisons with other ZIP12 sequences showed that the rat ZIP12 protein sequence [GenBank: NP_001099594] was likely missing the N-terminus (Figure S3). As a result, the N-terminus of ZIP12 in this report was reconstituted from the translated sequences of a rat EST [GenBank: FM065041] and 12 nucleotides of the rat genome [GenBank: NW_047496 3955687-3955698] (Figure 4, Figure S3). The 5′ untranslated region (UTR) of the annotated cow ZIP12 [GenBank: NM_001076878] (Figure 5) is missing at least 60 bp, based upon EST data and the observation that the conserved exon-intron structure of human, mouse, and chicken slc39a12 has the start codon in exon 2 (Figure 1, Figure 2). A comparison of the 5′ end of 2 EST clones [GenBank: EV626550 and EE901356] aligns to a separate exon in the cow genome [GenBank: AC_000170, 32666526-32666609]. The refinement of draft genome sequences and the correct annotation of gene sequences is important because genome sequences often provide the initial foundation for biological experimentation, particularly in reverse genetics.

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