Evolutionary genetics of an alternative molecular mechanism of hypoxia response in metazoans

可用氧气水平降低的环境对动物施加了高度紧张的条件。由于全球气候变化，海洋沃茨缺氧的频率和严重程度迅速增加，对包括普通鱼类和甲壳类在内的海洋生物种群产生了不利影响。在动物中，缺氧导致明显的细胞生理反应，这些反应由一套称为缺氧诱导因子（HIF）途径的主调节基因控制。HIF途径已在许多动物群体中被广泛研究，并被假设在所有物种中是保守的。然而，最近对海洋甲壳类动物的基因组分析显示，一些常见和丰富的物种已经失去了这组基因，但仍然非常耐受暂时的缺氧条件。因此，这些物种已经进化出一种不同的，但仍然未知的处理缺氧的遗传机制。发现和表征这些新的细胞和遗传过程是该项目的主要重点，将为动物如何适应压力环境提供更广泛和更完整的理解。研究人员将通过多种途径吸引第一代或代表性不足的STEM群体的本科生，包括鼓励他们参与项目的所有阶段，从数据收集到会议演示和出版，以及与路易斯·斯托克斯少数民族参与联盟（LSAMP）合作协调各种研究和培训讲习班我们如何理解与动物如何处理缺氧相关的遗传和生理过程，已经从具有HIF调节机制的物种中了解到。该项目将研究潮间带桡足类Tigriopus californicus缺氧反应的替代遗传机制，Tigriopus californicus是最近被证明已经失去HIF途径的物种之一，但仍然表现出对极端缺氧条件的强大耐受性。这项工作的一个主要目标是揭示哪些转录因子已经进化来填补HIF-1在其缺失时的作用，以及哪些生理反应由这些新的主调节因子控制。开放的染色质区域的位置将被确定在缺氧胁迫下的桡足类，这将允许候选转录因子的计算预测。定量和功能遗传实验将使用自然种群（捕获对环境缺氧的长期适应）和选择增加缺氧耐受性的实验室种群（具有强选择的短期适应）。在实验方法中，全基因组测序将用于绘制与缺氧反应中的自然变异相关的基因座，以及量化实验室进化过程中等位基因频率的轨迹。最后，重组近交系将被用来估计基因共表达网络和测试相关的生理表型与缺氧反应转录模块。该项目的发现可能会揭示以前未知的基因的重要功能，以及基因和蛋白质相互作用以在低氧胁迫下维持体内平衡的新方式。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

Environments with decreased levels of available oxygen impose highly stressful conditions for animals. Exacerbated by global climate change, hypoxia in ocean waters has been rapidly increasing in frequency and severity, and this has adversely affected populations of marine organisms, including common fishes and crustaceans. In animals, hypoxia results in pronounced cellular physiological responses that are controlled by a suite of master regulatory genes, called the hypoxia-inducible factor (HIF) pathway. The HIF pathway has been widely studied in many groups of animals and was hypothesized to be conserved in all species. Very recent genomic analyses in marine crustaceans, however, revealed that several common and abundant species have lost this set of genes, but are still very tolerant to temporary hypoxic conditions. These species therefore have evolved a different yet still unknown genetic mechanism of dealing with hypoxia. Discovering and characterizing these novel cellular and genetic processes is the main focus of this project and will provide a broader and more complete understanding of how animals adapt to stressful environments. The researchers will engage undergraduate students from first-generation or underrepresented groups in STEM through multiple routes, including encouraging participation in all stages of the project, from data collection to conference presentation and publication, as well as coordinating various research and training workshops in conjunction with the Louis Stokes Alliance for Minority Participation (LSAMP) program at OSU.How we understand the genetic and physiological processes associated with how animals deal with hypoxia have been learned from species with the HIF regulatory machinery. This project will investigate alternative genetic mechanisms of hypoxia response in the intertidal copepod Tigriopus californicus, which is one of the species recently shown to have lost the HIF pathway, but which still exhibit robust tolerance to extreme hypoxic conditions. A major goal of the work is to unmask what transcription factors have evolved to fill the role of HIF-1 in its absence, and what physiological responses are controlled by these new master regulators. The location of open chromatin regions will be identified in copepods under hypoxic stress, which will permit computational prediction of candidate transcription factors. Quantitative and functional genetic experiments will use both natural populations (capturing long term adaptation to environmental hypoxia) and lab populations selected for increased hypoxia tolerance (short term adaptation with strong selection). Among experimental approaches, whole genome sequencing will be used to map loci associated with natural variation in hypoxia response as well as to quantify the trajectory of allele frequencies during laboratory evolution. Finally, recombinant inbred lines will be used to estimate gene co-expression networks and to test correlations of physiological phenotypes with hypoxia-response transcription modules. Findings of this project will likely reveal important functions for previously unknown genes and new ways in which genes and proteins interact to maintain homeostasis during low oxygen stress.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.