Genome wide identification, phylogeny and expression of zinc transporter genes in common carp

Abstract

Background: Zinc is an essential trace element in organisms, which serves as a cofactor for hundreds of enzymes that are involved in many pivotal biological processes including growth, development, reproduction and immunity. Therefore, the homeostasis of zinc in the cell is fundamental. The zinc transporter gene family is a large gene family that encodes proteins which regulate the movement of zinc across cellular and intracellular membranes. However, studies on teleost zinc transporters are mainly limited to model species.

Methodology/principal findings: We identified a set of 37 zinc transporters in common carp genome, including 17 from SLC30 family (ZnT), and 20 from SLC39 family (ZIP). Phylogenetic and syntenic analysis revealed that most of the zinc transporters are highly conserved, though recent gene duplication and gene losses do exist. Through examining the copy number of zinc transporter genes across several vertebrate genomes, thirteen zinc transporters in common carp are found to have undergone the gene duplications, including SLC30A1, SLC30A2, SLC30A5, SLC30A7, SLC30A9, SLC30A10, SLC39A1, SLC39A3, SLC39A4, SLC39A5, SLC39A6, SLC39A7 and SLC39A9. The expression patterns of all zinc transporters were established in various tissues, including blood, brain, gill, heart, intestine, liver, muscle, skin, spleen and kidney, and showed that most of the zinc transporters were ubiquitously expressed, indicating the critical role of zinc transporters in common carp.

Conclusions: To some extent, examination of gene families with detailed phylogenetic or orthology analysis could verify the authenticity and accuracy of assembly and annotation of the recently published common carp whole genome sequences. The gene families are also considered as a unique source for evolutionary studies. Moreover, the whole set of common carp zinc transporters provides an important genomic resource for future biochemical, toxicological and physiological studies of zinc in teleost.

Figure 1. Schematic representation of the domain architecture of zinc transporters in common carp.

TM represents the transmembrane region; RPT represents the internal repeat 1; BLAST represents the domain present in proteins and involved in regulation of nuclear pre-mRNA; SCOP represents the putative copper-binding protein; DUF4554 represents the domain of unknown function 4554; and Yippee-Mis18 represents the Yippee zinc-binding/DNA-binding/Mis18.

Figure 2. The common carp zinc transporter gene family.

Numbers around the nodes correspond to bootstrap support values. Abbreviations: H: Homo sapiens; Z: Danio rerio and C: Cyprinus carpio. The black dots/diamonds indicate common carp genes.

Figure 3. Phylogenetic tree of SLC30 family transporters.

The phylogenetic tree was constructed using maximum likelihood algorithm under the JTT+I+G model of amino acid substitution as described in detail in Materials and Methods section. Numbers around the nodes correspond to bootstrap support values in percentages.

Figure 4. Analysis of conserved synteny blocks harboring SLC30A7 gene in several vertebrates.

Horizontal lines denote orthologous relationships. Abbreviations: s1pr1: Sphingosine 1-phosphate receptor 1; dph5: Diphthine synthase 5; slc30a7: Solute-carrier gene family 30, member 7; vcam1: Vascular cell adhesion protein 1; gpr88: Probable G-protein coupled receptor 88; cdc14a: Cell division cycle 14 homolog A; rtca: RNA 3′-terminal phosphate cyclase; dbt: Dihydrolipoamide branched chain transacylase; lrrc39: Leucine rich repeat containing 39.

Figure 5. Analysis of conserved synteny blocks harboring SLC30A1 gene in several vertebrates.

Horizontal lines denote orthologous relationships. Abbreviations: lpgat1: Lysophosphatidylglycerol acyltransferase 1; nek2: NIMA (never in mitosis gene a)-related kinase 2; slc30a1: Solute-carrier gene family 30, member 1; rd3: Retinal degeneration 3; rhag: Rhesus blood group-associated glycoprotein; kcns3: Potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3.

Figure 6. Phylogenetic tree of SLC39 family transporters.

The phylogenetic tree was obtained as in Fig. 3. Numbers around the nodes correspond to bootstrap support values.

Figure 7. RT-PCR based expression analysis of common carp zinc transporter genes.

The amplification of β-actin was used as an internal control. Gene names are indicated on the left of the panel.