Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes.
Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes.
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修饰的碱基结合的Eve和DCD结构域：原核生物基因组环境的惊人多样性，并预测参与各种细胞过程。
DOI：
10.1186/s12915-020-00885-2
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发表时间：
2020-11-04
期刊：
影响因子：
5.4
通讯作者：
Koonin EV
中科院分区：
文献类型：
--
作者：
Bell RT;Wolf YI;Koonin EV
所有细胞生命形式和许多病毒的DNA和RNA都含有大量的修饰碱基。修饰的碱基发挥多种生物学作用，包括转录和翻译的调节，以及对限制性内切酶和抗生素的保护。修饰的碱基通常被专用的蛋白质结构域识别。然而，由修饰的碱基介导的相互作用和过程的复杂网络远未被完全理解。我们提出了一个全面的普查和分类的EVE域属于普阿/ASCH域超家族，并结合各种修饰的DNA和RNA中的碱基。我们采用的“内疚协会”的方法，使功能推断细菌和古细菌基因组的比较分析，基于分布和协会的EVE域（预测）操纵子和功能网络的基因。原核生物编码两类EVE结构域蛋白，缓慢进化和快速进化的。在α-变形菌中，缓慢进化的EVE结构域嵌入保守的操纵子中，通过结合tRNA中的5-甲基胞嘧啶，可能参与翻译和呼吸之间的偶联，特别是细胞色素c的生物合成。在β-和γ-变形菌中，保守的关联暗示EVE结构域在细胞分裂、生物膜形成和通过非编码6S小RNA的全局转录调节中的协调，所述非编码6S小RNA可能被EVE结构域修饰和结合。在真核生物中，含有EVE结构域的THYN 1样蛋白已被报道可能通过结合DNA和/或RNA中的5-甲基胞嘧啶及其衍生物来抑制PCD和调节细胞周期。我们假设PCD和细胞色素c之间的联系是从α-变形菌和原线粒体内共生体遗传的，并且出乎意料地，可能涉及EVE结构域的修饰碱基识别。快速进化的EVE结构域通常嵌入在防御环境中，包括毒素-抗毒素模块和IV型限制系统，这表明在入侵DNA分子中识别修饰的碱基并将其靶向限制的作用。我们还鉴定了EVE-like原核发育和细胞死亡（DCD）结构域，这些结构域也涉及包括PCD在内的防御功能。这种功能被真核生物继承，但在动物中，DCD蛋白显然被扩展的Tudor家族蛋白取代，其与Piwi相关的Argonautes的伙伴关系成为Piwi相互作用RNA（皮尔纳）系统的核心。通过EVE-like结构域识别DNA和RNA中修饰的碱基似乎是一个重要的，但直到现在，未被充分认识的，在各种过程中的共同点，包括PCD，细胞周期控制，抗病毒免疫，应激反应，和动物的生殖系发育。
DNA and RNA of all cellular life forms and many viruses contain an expansive repertoire of modified bases. The modified bases play diverse biological roles that include both regulation of transcription and translation, and protection against restriction endonucleases and antibiotics. Modified bases are often recognized by dedicated protein domains. However, the elaborate networks of interactions and processes mediated by modified bases are far from being completely understood. We present a comprehensive census and classification of EVE domains that belong to the PUA/ASCH domain superfamily and bind various modified bases in DNA and RNA. We employ the “guilt by association” approach to make functional inferences from comparative analysis of bacterial and archaeal genomes, based on the distribution and associations of EVE domains in (predicted) operons and functional networks of genes. Prokaryotes encode two classes of EVE domain proteins, slow-evolving and fast-evolving ones. Slow-evolving EVE domains in α-proteobacteria are embedded in conserved operons, potentially involved in coupling between translation and respiration, cytochrome c biogenesis in particular, via binding 5-methylcytosine in tRNAs. In β- and γ-proteobacteria, the conserved associations implicate the EVE domains in the coordination of cell division, biofilm formation, and global transcriptional regulation by non-coding 6S small RNAs, which are potentially modified and bound by the EVE domains. In eukaryotes, the EVE domain-containing THYN1-like proteins have been reported to inhibit PCD and regulate the cell cycle, potentially, via binding 5-methylcytosine and its derivatives in DNA and/or RNA. We hypothesize that the link between PCD and cytochrome c was inherited from the α-proteobacterial and proto-mitochondrial endosymbiont and, unexpectedly, could involve modified base recognition by EVE domains. Fast-evolving EVE domains are typically embedded in defense contexts, including toxin-antitoxin modules and type IV restriction systems, suggesting roles in the recognition of modified bases in invading DNA molecules and targeting them for restriction. We additionally identified EVE-like prokaryotic Development and Cell Death (DCD) domains that are also implicated in defense functions including PCD. This function was inherited by eukaryotes, but in animals, the DCD proteins apparently were displaced by the extended Tudor family proteins, whose partnership with Piwi-related Argonautes became the centerpiece of the Piwi-interacting RNA (piRNA) system. Recognition of modified bases in DNA and RNA by EVE-like domains appears to be an important, but until now, under-appreciated, common denominator in a variety of processes including PCD, cell cycle control, antivirus immunity, stress response, and germline development in animals.
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影响因子：
2.9
作者：
Bertonati, Claudia;Punta, Marco;Fischer, Markus;Yachdav, Guy;Forouhar, Farhad;Zhou, Weihong;Kuzin, Alexander P.;Seetharaman, Jayaraman;Abashidze, Mariam;Ramelot, Theresa A.;Kennedy, Michael A.;Cort, John R.;Belachew, Adam;Hunt, John F.;Tong, Liang;Montelione, Gaetano T.;Rost, Burkhard
通讯作者：
Rost, Burkhard
影响因子：
4.4
作者：
Anders M;Chelysheva I;Goebel I;Trenkner T;Zhou J;Mao Y;Verzini S;Qian SB;Ignatova Z
通讯作者：
Ignatova Z
影响因子：
3.9
作者：
Aravind, L;Koonin, EV
通讯作者：
Koonin, EV
影响因子：
3.2
作者：
ALDEA, M;HERNANDEZCHICO, C;VICENTE, M
通讯作者：
VICENTE, M
影响因子：
7.2
作者：
Compton, MM;Thomson, JM;Icard, AH
通讯作者：
Icard, AH