Data from: Analysis of hypoxia-inducible factor alpha polyploidization reveals adaptation to Tibetan plateau in the evolution of schizothoracine fish

Background: Hypoxia-inducible factor (HIF) is a master regulator that mediates major changes in gene expression under hypoxic conditions. Though HIF family has been identified in many organisms, little is known about this family in schizothoracine fish. Results: Duplicated hif-α (hif-1αA, hif-1αB, hif-2αA, and hif-2αB) genes were identified in schizothoracine fish. All the deduced HIF-α proteins contain the main domains (bHLH-PAS, ODDD, and TAD), also found in humans. Evidence suggests a Cyprinidae-specific deletion, specifically, a conserved proline hydroxylation motif LxxLAP, in the NODD domain of schizothoracine fish HIF-1αA. In addition, a schizothoracine-specific mutation was observed in the CODD domain of the specialized and highly specialized schizothoracine fish HIF-1αB, which is the proline hydroxylation motif mutated into PxxLAP. Standard and stochastic branch-site codon model analysis indicated that only HIF-1αB has undergone positive selection, which may have led to changes in function. To confirm this hypothesis, HIF-αs tagged with Myc were transfected into HEK 293 T cells. Each HIF-1αB was found to significantly upregulate luciferase activity under normoxic and hypoxic conditions, which indicated that the HIF-1αB protein was more stable than other HIF-αs. Conclusions: All deduced HIF-α proteins of schizothoracine fish contain important domains, like their mammalian counterparts, and each HIF-α is shorter than that of human. Our experiments reveal that teleost-specific duplicated hif-α genes played different roles under hypoxic conditions, and HIF-1αB may be the most important regulator in the adaptation of schizothoracine fish to the environment of the Tibetan Plateau.

背景：缺氧诱导因子（Hypoxia-inducible factor, HIF）是介导缺氧条件下基因表达发生显著变化的核心调控因子。尽管已在多种生物中鉴定出HIF家族成员，但目前对裂腹鱼（schizothoracine fish）中该家族的了解仍十分有限。结果：研究人员在裂腹鱼中鉴定出了复制型hif-α基因（hif-1αA、hif-1αB、hif-2αA及hif-2αB）。所有推导得到的HIF-α蛋白均包含核心结构域（bHLH-PAS、ODDD及TAD），这些结构域在人类蛋白中同样存在。研究证据显示，裂腹鱼HIF-1αA的NODD结构域中存在鲤科（Cyprinidae）特异性缺失，具体为保守的脯氨酸羟化基序LxxLAP的缺失。此外，在特化及高度特化裂腹鱼的HIF-1αB的CODD结构域中，观察到了裂腹鱼特异性突变：其脯氨酸羟化基序突变为PxxLAP。通过标准分支位点密码子模型与随机分支位点密码子模型开展分析，结果表明仅HIF-1αB经历了正向选择，这一过程可能引发其功能改变。为验证该假说，研究人员将带有Myc标签的HIF-α基因转染至人胚肾293T（HEK 293 T）细胞中。实验发现，在常氧与缺氧条件下，各HIF-1αB均能显著上调荧光素酶活性，这提示HIF-1αB蛋白相较于其他HIF-α蛋白具有更高的稳定性。结论：裂腹鱼所有推导得到的HIF-α蛋白均包含重要结构域，与其哺乳动物同源物一致，且各HIF-α蛋白的长度均短于人类同源蛋白。本研究实验结果显示，硬骨鱼特异性复制的hif-α基因在缺氧条件下发挥着不同的功能，而HIF-1αB可能是裂腹鱼适应青藏高原环境的核心调控因子。