Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria.
Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria.
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DOI：
10.1038/s41467-022-35523-8
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发表时间：
2022-12-21
影响因子：
16.6
通讯作者：
Xiao, Xiang
中科院分区：
文献类型：
--
作者：
Zhao, Weishu;Zhong, Bozitao;Zheng, Lirong;Tan, Pan;Wang, Yinzhao;Leng, Hao;de Souza, Nicolas;Liu, Zhuo;Hong, Liang;Xiao, Xiang
由于缺乏基于序列的重建以外的证据，祖先的新陈代谢一直存在争议。尽管益生菌化学家提供了代谢可能起源于非酶原代谢途径的线索，但祖先重建和益生菌过程之间的差距意味着仍有许多未知之处。在这里，我们应用蛋白质组范围的3D结构预测和比较来研究古代细菌和古菌的祖先新陈代谢，以提供序列以外的信息作为通往益生过程的桥梁。我们比较了代表性的细菌和古细菌菌株，它们通过微生物学和生物物理实验显示出惊人的相似的生理和代谢特征。蛋白质结构的成对比较确定了细菌和古菌中保守的代谢模块，尽管受到过度可变的序列的干扰。保守的模块(如糖酵解中间、部分TCA、质子/硫呼吸、积木生物合成)构成了古生菌-细菌共同祖先可能存在的基本功能，与实验证实的原代谢途径非常一致。这些基于结构的发现为重建祖先代谢和了解其起源提供了新的视角，这表明高通量蛋白质三维结构预测是一种很有前途的方法，值得在未来的祖先探索中得到更广泛的应用。以前的研究已经使用基于序列的方法重建了祖先的新陈代谢。这项研究使用高通量版本的AlphaFold2来比较古细菌和细菌两个代表菌株的蛋白质组范围的3D结构预测。
Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration. Previous studies have reconstructed ancestral metabolism using sequence-based approaches. This study uses a high-throughput version of AlphaFold2 to compare proteome-wide 3D structure predictions of two representative strains of ancient archaea and bacteria.
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影响因子：
64.8
作者：
Jumper J;Evans R;Pritzel A;Green T;Figurnov M;Ronneberger O;Tunyasuvunakool K;Bates R;Žídek A;Potapenko A;Bridgland A;Meyer C;Kohl SAA;Ballard AJ;Cowie A;Romera-Paredes B;Nikolov S;Jain R;Adler J;Back T;Petersen S;Reiman D;Clancy E;Zielinski M;Steinegger M;Pacholska M;Berghammer T;Bodenstein S;Silver D;Vinyals O;Senior AW;Kavukcuoglu K;Kohli P;Hassabis D
通讯作者：
Hassabis D
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
5.7
作者：
Cisse, Aline;Schachner-Nedherer, Anna-Laurence;Peters, Judith
通讯作者：
Peters, Judith
影响因子：
64.8
作者：
Boussau, Bastien;Blanquart, Samuel;Gouy, Manolo
通讯作者：
Gouy, Manolo
影响因子：
11
作者：
Gu, Jiahao;Wang, Xiaojun;Luo, Haiwei
通讯作者：
Luo, Haiwei