Hypoxia Inducible Factor (HIF) transcription factor family expansion, diversification, divergence and selection in eukaryotes

Hypoxia inducible factor (HIF) transcription factors are crucial for regulating a variety of cellular activities in response to oxygen stress (hypoxia). In this study, we determine the evolutionary history of HIF genes and their associated transactivation domains, as well as perform selection and functional divergence analyses across their four characteristic domains. Here we show that the HIF genes are restricted to metazoans: At least one HIF-α homolog is found within the genomes of non-bilaterians and bilaterian invertebrates, while most vertebrate genomes contain between two and six HIF-α genes. We also find widespread purifying selection across all four characteristic domain types, bHLH, PAS, NTAD, CTAD, in HIF-α genes, and evidence for Type I functional divergence between HIF-1α, HIF-2α /EPAS, and invertebrate HIF genes. Overall, we describe the evolutionary histories of the HIF transcription factor gene family and its associated transactivation domains in eukaryotes. We show that the NTAD and CTAD domains appear de novo, without any appearance outside of the HIF-α subunits. Although they both appear in invertebrates as well as vertebrate HIF- α sequences, there seems to have been a substantial loss across invertebrates or were convergently acquired in these few lineages. We reaffirm that HIF-1α is phylogenetically conserved among most metazoans, whereas HIF-2α appeared later. Overall, our findings can be attributed to the substantial integration of this transcription factor family into the critical tasks associated with maintenance of oxygen homeostasis and vascularization, particularly in the vertebrate lineage.

缺氧诱导因子（hypoxia inducible factor, HIF）转录因子在响应氧应激（缺氧）过程中调控多种细胞活动，发挥关键作用。本研究明确了HIF基因及其相关反式激活结构域（transactivation domain）的进化历程，并针对其四类特征性结构域开展选择压力与功能分化分析。研究结果显示，HIF基因仅存在于后生动物（metazoan）中：非两侧对称动物（non-bilaterian）与两侧对称无脊椎动物（bilaterian invertebrate）的基因组内至少存在一个HIF-α同源基因，而多数脊椎动物基因组则包含2至6个HIF-α基因。此外，我们在HIF-α基因的四类特征性结构域（bHLH、PAS、NTAD、CTAD）中均检测到广泛存在的纯化选择（purifying selection）信号，同时在HIF-1α、HIF-2α/EPAS与无脊椎动物HIF基因之间发现I型功能分化（Type I functional divergence）的证据。综上，本研究阐明了真核生物中HIF转录因子基因家族及其相关反式激活结构域的进化历程。研究发现NTAD与CTAD结构域为从头起源，仅存在于HIF-α亚基中，未在其他蛋白亚基中被观测到。尽管这两类结构域在无脊椎动物与脊椎动物的HIF-α序列中均有出现，但它们在无脊椎动物中似乎发生了大规模丢失，或是仅在少数无脊椎动物谱系中通过趋同演化获得。本研究进一步证实，HIF-1α在多数后生动物中系统发育保守，而HIF-2α的出现时间相对较晚。综上，本研究的结论可归因于该转录因子家族已深度整合到维持氧稳态（oxygen homeostasis）与血管生成（vascularization）的核心生物学过程中，这一特征在脊椎动物谱系中尤为显著。