Karanth Santhosh, Lall Santosh P, Denovan-Wright Eileen M, Wright Jonathan M
Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, Canada.
BMC Evol Biol. 2009 Sep 2;9:219. doi: 10.1186/1471-2148-9-219.
In the Duplication-Degeneration-Complementation (DDC) model, subfunctionalization and neofunctionalization have been proposed as important processes driving the retention of duplicated genes in the genome. These processes are thought to occur by gain or loss of regulatory elements in the promoters of duplicated genes. We tested the DDC model by determining the transcriptional induction of fatty acid-binding proteins (Fabps) genes by dietary fatty acids (FAs) in zebrafish. We chose zebrafish for this study for two reasons: extensive bioinformatics resources are available for zebrafish at zfin.org and zebrafish contains many duplicated genes owing to a whole genome duplication event that occurred early in the ray-finned fish lineage approximately 230-400 million years ago. Adult zebrafish were fed diets containing either fish oil (12% lipid, rich in highly unsaturated fatty acid), sunflower oil (12% lipid, rich in linoleic acid), linseed oil (12% lipid, rich in linolenic acid), or low fat (4% lipid, low fat diet) for 10 weeks. FA profiles and the steady-state levels of fabp mRNA and heterogeneous nuclear RNA in intestine, liver, muscle and brain of zebrafish were determined.
FA profiles assayed by gas chromatography differed in the intestine, brain, muscle and liver depending on diet. The steady-state level of mRNA for three sets of duplicated genes, fabp1a/fabp1b.1/fabp1b.2, fabp7a/fabp7b, and fabp11a/fabp11b, was determined by reverse transcription, quantitative polymerase chain reaction (RT-qPCR). In brain, the steady-state level of fabp7b mRNAs was induced in fish fed the linoleic acid-rich diet; in intestine, the transcript level of fabp1b.1 and fabp7b were elevated in fish fed the linolenic acid-rich diet; in liver, the level of fabp7a mRNAs was elevated in fish fed the low fat diet; and in muscle, the level of fabp7a and fabp11a mRNAs were elevated in fish fed the linolenic acid-rich or the low fat diets. In all cases, induction of the steady-state level of fabp mRNAs by dietary FAs correlated with induced levels of hnRNA for a given fabp gene. As such, up-regulation of the steady-state level of fabp mRNAs by FAs occurred at the level of initiation of transcription. None of the sister duplicates of these fabp genes exhibited an increase in their steady-state transcript levels in a specific tissue following feeding zebrafish any of the four experimental diets.
Differential induction of only one of the sister pair of duplicated fabp genes by FAs provides evidence to support the DDC model for retention of duplicated genes in the zebrafish genome by either subfunctionalization or neofunctionalization.
在复制-退化-互补（DDC）模型中，亚功能化和新功能化被认为是驱动基因组中重复基因保留的重要过程。这些过程被认为是通过重复基因启动子中调控元件的获得或丧失而发生的。我们通过测定斑马鱼中膳食脂肪酸（FAs）对脂肪酸结合蛋白（Fabps）基因的转录诱导来测试DDC模型。我们选择斑马鱼进行这项研究有两个原因：在zfin.org网站上可获得大量关于斑马鱼的生物信息学资源，并且由于大约2.3亿至4亿年前在硬骨鱼谱系早期发生的全基因组复制事件，斑马鱼含有许多重复基因。成年斑马鱼被喂食含有鱼油（12%脂质，富含高度不饱和脂肪酸）、向日葵油（12%脂质，富含亚油酸）、亚麻籽油（12%脂质，富含亚麻酸）或低脂（4%脂质，低脂饮食）的饲料，持续10周。测定了斑马鱼肠道、肝脏、肌肉和大脑中的脂肪酸谱以及fabp mRNA和异质核RNA的稳态水平。
通过气相色谱法测定的脂肪酸谱在肠道、大脑、肌肉和肝脏中因饮食而异。通过逆转录定量聚合酶链反应（RT-qPCR）测定了三组重复基因fabp1a/fabp1b.1/fabp1b.2、fabp7a/fabp7b和fabp11a/fabp11b的mRNA稳态水平。在大脑中，喂食富含亚油酸饮食的鱼中fabp7b mRNA的稳态水平升高；在肠道中，喂食富含亚麻酸饮食的鱼中fabp1b.1和fabp7b的转录水平升高；在肝脏中，喂食低脂饮食的鱼中fabp7a mRNA的水平升高；在肌肉中，喂食富含亚麻酸或低脂饮食的鱼中fabp7a和fabp11a mRNA的水平升高。在所有情况下，膳食脂肪酸对fabp mRNA稳态水平的诱导与给定fabp基因的hnRNA诱导水平相关。因此，脂肪酸对fabp mRNA稳态水平的上调发生在转录起始水平。在给斑马鱼喂食四种实验饲料中的任何一种后，这些fabp基因的任何一对姐妹重复基因在特定组织中的稳态转录水平均未增加。
脂肪酸对重复的fabp基因姐妹对中仅一个的差异诱导为支持DDC模型提供了证据，该模型认为通过亚功能化或新功能化，重复基因得以保留在斑马鱼基因组中。
