Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota
Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota
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比较基因组推断表明胸古菌的混合营养生活方式
DOI：
10.1038/s41396-018-0060-x
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发表时间：
2018-04-01
期刊：
影响因子：
11
通讯作者：
Li, Meng
中科院分区：
文献类型：
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作者：
Liu, Yang;Zhou, Zhichao;Li, Meng
胸古菌是阿斯加德超门中一个新的古菌门，其祖先在细胞进化中可能起着生态作用。然而，人们对这些未经培养的古生菌的生活方式知之甚少。为了更好地解析Thorarchaeota的生态作用和代谢能力，我们从红树林和泥滩沉积物的不同深度层的宏基因组中重建了Thorarchaeota基因组。这些来自深层缺氧层的基因组表明，Thorarchaeota的存在具有降解有机物、固定无机碳、减少硫/硫酸盐和产生醋酸盐的潜力。特别是，胸古菌可能参与乙醇生产、固氮、亚硝酸盐还原和砷解毒。有趣的是，这些Thorarchaeotal基因组被推断包含用于二氧化碳还原的四氢甲烷蝶呤和四氢叶酸Wood-Ljungdahl （WL）途径，后者的WL途径似乎起源于细菌。据预测，这些古细菌能够利用各种无机和有机碳源，拥有编码二磷酸核酮糖羧化酶样蛋白的基因（通常没有RuBisCO活性）和一个近乎完整的Calvin-Benson-Bassham循环。真核硒代半胱氨酸插入序列和许多先前被认为是真核特异性蛋白质的基因的存在，为它们在真核细胞复杂性起源中的进化作用提供了新的见解。解决这些神秘的古细菌及其起源的代谢能力将增强我们对真核生物起源及其在生态系统中的作用的理解。
Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen fixation, nitrite reduction, and arsenic detoxification. Interestingly, these Thorarchaeotal genomes are inferred to contain the tetrahydromethanopterin and tetrahydrofolate Wood–Ljungdahl (WL) pathways for CO2reduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisphosphate carboxylase-like proteins (normally without RuBisCO activity) and a near-complete Calvin–Benson–Bassham cycle. The existence of eukaryotic selenocysteine insertion sequences and many genes for proteins previously considered eukaryote-specific in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryotic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their roles in ecosystems.