Tissue-specific differential induction of duplicated fatty acid-binding protein genes by the peroxisome proliferator, clofibrate, in zebrafish (Danio rerio)

Ananda B Venkatachalam,Jonathan M Wright,Santosh P Lall,Eileen M Denovan-Wright

doi:10.1186/1471-2148-12-112

Ananda B Venkatachalam, Jonathan M Wright + Show 2 more

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https://doi.org/10.1186/1471-2148-12-112

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Abstract

BackgroundForce, Lynch and Conery proposed the duplication-degeneration-complementation (DDC) model in which partitioning of ancestral functions (subfunctionalization) and acquisition of novel functions (neofunctionalization) were the two primary mechanisms for the retention of duplicated genes. The DDC model was tested by analyzing the transcriptional induction of the duplicated fatty acid-binding protein (fabp) genes by clofibrate in zebrafish. Clofibrate is a specific ligand of the peroxisome proliferator-activated receptor (PPAR); it activates PPAR which then binds to a peroxisome proliferator response element (PPRE) to induce the transcriptional initiation of genes primarily involved in lipid homeostasis. Zebrafish was chosen as our model organism as it has many duplicated genes owing to a whole genome duplication (WGD) event that occurred ~230-400 million years ago in the teleost fish lineage. We assayed the steady-state levels of fabp mRNA and heterogeneous nuclear RNA (hnRNA) transcripts in liver, intestine, muscle, brain and heart for four sets of duplicated fabp genes, fabp1a/fabp1b.1/fabp1b.2, fabp7a/fabp7b, fabp10a/fabp10b and fabp11a/fabp11b in zebrafish fed different concentrations of clofibrate.ResultElectron microscopy showed an increase in the number of peroxisomes and mitochondria in liver and heart, respectively, in zebrafish fed clofibrate. Clofibrate also increased the steady-state level of acox1 mRNA and hnRNA transcripts in different tissues, a gene with a functional PPRE. These results demonstrate that zebrafish is responsive to clofibrate, unlike some other fishes. The levels of fabp mRNA and hnRNA transcripts for the four sets of duplicated fabp genes was determined by reverse transcription, quantitative polymerase chain reaction (RT-qPCR). The level of hnRNA coded by a gene is an indirect estimate of the rate of transcriptional initiation of that gene. Clofibrate increased the steady-state level of fabp mRNAs and hnRNAs for both the duplicated copies of fabp1a/fabp1b.1, and fabp7a/fabp7b, but in different tissues. Clofibrate also increased the steady-state level of fabp10a and fabp11a mRNAs and hnRNAs in liver, but not for fabp10b and fabp11b.ConclusionSome duplicated fabp genes have, most likely, retained PPREs, but induction by clofibrate is over-ridden by an, as yet, unknown tissue-specific mechanism(s). Regardless of the tissue-specific mechanism(s), transcriptional control of duplicated zebrafish fabp genes by clofibrate has markedly diverged since the WGD event.

Highlights

Force, Lynch and Conery proposed the duplication-degeneration-complementation (DDC) model in which partitioning of ancestral functions and acquisition of novel functions were the two primary mechanisms for the retention of duplicated genes
Changes in the levels of mRNA for a specific fabp gene were directly correlated with changes in the steady-state level of heterogeneous nuclear RNA (hnRNA) for that particular fabp gene indicating that clofibrate induced transcriptional initiation of zebrafish fabp genes (Table 1)
Clofibrate induction of some zebrafish fabp genes appears, to be controlled by a tissue-specific mechanism(s), as induction of the steady-state level of fabp mRNAs and hnRNAs by clofibrate was seen for both duplicated fabpf7aabpm7RaN- ALiv-eLriver fabfapb7pb7mbR- NLiAve-r Liver

Summary

Introduction

Lynch and Conery proposed the duplication-degeneration-complementation (DDC) model in which partitioning of ancestral functions (subfunctionalization) and acquisition of novel functions (neofunctionalization) were the two primary mechanisms for the retention of duplicated genes. Neofunctionalization results from mutations in the protein coding region that gives rise to a novel function for a gene product. With complete genomic DNA sequences becoming increasingly available, it is apparent that a greater proportion of gene duplicates are preserved in genomes than that predicted by Ohno’s model [6]. In light of these observations, Force et al [6], subsequently elaborated by Lynch and Conery [7], proposed the duplication-degeneration-complementation (DDC) model. In the DDC model, subfunctionalization and neofunctionalization occur by either loss or gain of cis-regulatory elements in the promoters of the duplicated genes

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