Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages.
Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages.
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DOI：
10.1038/s43705-021-00032-0
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发表时间：
2021-06-28
期刊：
影响因子：
--
通讯作者：
Wilmes, Paul
中科院分区：
文献类型：
--
作者：
Busi, Susheel Bhanu;de Nies, Laura;Habier, Janine;Wampach, Linda;Fritz, Joelle V.;Heintz-Buschart, Anna;May, Patrick;Halder, Rashi;de Beaufort, Carine;Wilmes, Paul
asgardarchaaeota被认为是真核生物的近亲，迄今为止，共有72个宏基因组组装基因组（MAGs）代表了该古细菌门的6个主要谱系。这些生物被预测为促进沉积物生态系统碳循环的发酵异养生物。在这里，我们通过从全球范围内的栖息地获得71个mag，包括深层地下，咸淡浅湖和地热泉沉积物，将asgardarchaaeota的基因组目录翻了一番。系统基因组学推断和分类等级归一化证实了先前建立的asgardarchaaeota分类，并揭示了另外四个谱系，其中两个一直被恢复为单系分类。因此，我们建议将其命名为Candidatus Sifarchaeia class nov和Ca. Jordarchaeia class nov，这两个名字来源于挪威神话中的神Sif和Jord。代谢推断表明，这两类都代表了异有机营养醋酸菌，它们也具有利用甲基化胺等甲基的能力，乙酸可能是甲烷菌衍生的核心代谢残留物的最终产物。这种推断的能量守恒模式预计会通过遗传密码扩展而增强，即停止密码子重新编码，从而允许罕见的第21和第22氨基酸硒代半胱氨酸（Sec）和pyrlysine （Pyl）的加入。我们发现在Jordarchaeia和所有其他asgardarchaaoia类中都有Sec编码，这可能得益于含Sec酶的催化活性增加。另一方面，Pyl编码仅限于asgardarchaeia中的Sifarchaeia，使其成为第一个报道的具有完整Pyl机制的非产甲烷古细菌谱系，可能为该类成员提供了有效的甲胺利用机制。此外，我们在这两个新描述的类别中发现了用于生物合成酯型脂质的酶，这是细菌和真核生物的特征，支持了混合醚-酯脂质是asgardarchaaeota共同特征的假设。
Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca. Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero-organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of bacteria and eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.
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影响因子：
1.8
作者：
Dridi B;Khelaifia S;Fardeau ML;Ollivier B;Drancourt M
通讯作者：
Drancourt M
影响因子：
2.7
作者：
Delmont TO;Eren AM
通讯作者：
Eren AM
影响因子：
3.3
作者：
Coleman, Gareth A.;Pancost, Richard D.;Williams, Tom A.
通讯作者：
Williams, Tom A.
影响因子：
9.2
作者：
Castelle, Cindy J.;Wrighton, Kelly C.;Banfield, Jillian F.
通讯作者：
Banfield, Jillian F.
DOI：
10.1155/2014/374146
发表时间：
2014
期刊：
Archaea (Vancouver, B.C.)
影响因子：
--
作者：
Borrel G;Gaci N;Peyret P;O'Toole PW;Gribaldo S;Brugère JF
通讯作者：
Brugère JF