RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea.
RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea.
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DOI：
10.1128/mbio.00561-17
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发表时间：
2017-05-09
期刊：
影响因子：
6.4
通讯作者：
Söll D
中科院分区：
文献类型：
--
作者：
Mukai T;Crnković A;Umehara T;Ivanova NN;Kyrpides NC;Söll D
地球上微生物所使用的遗传密码系统的多样性尚未得到阐明。已知某些产甲烷古菌采用半胱氨酸（Cys）生物合成和编码的替代系统; tRNACys首先通过O-磷酸丝氨酰-tRNA合成酶（SepRS）用磷酸丝氨酸（Sep）酰化，然后通过Sep-tRNA：Cys-tRNA合成酶（SepCysS）转化为Cys-tRNACys。在这项研究中，我们搜索了整合微生物基因组（IMG）系统和NCBI中的所有基因组和宏基因组蛋白质序列数据，以揭示SepRS和SepCysS蛋白质的新分支，这些蛋白质属于四个主要群体（DPANN，Euryarchaeota，TACK和Asgard）和两组细菌（“Parcubacteria”和Chloroflexi）中的不同古菌。细菌SepRS和SepCysS在体外用半胱氨酸装载细菌tRNACys物种。SepCysE的同源物是一种支架蛋白，有助于SepRS和SepCysS复合物在Euryarchaeota I类产甲烷菌中的组装，在几组TACK和Asgard古菌中发现，而C-末端截短的同源物与不同的SepCysS物种融合或遗传偶联。对利用SepRS的古细菌和细菌中硒代半胱氨酸（Sec）和吡咯赖氨酸（Pyl）利用性状的研究表明，携带全长SepCysE的古细菌利用Sec，SepRS通常存在于利用Pyl的古细菌和绿弯菌中。我们讨论了SepRS-SepCysS系统对硫同化、甲烷生成和其他需要大量铁硫酶或含Pyl酶的代谢过程的可能贡献。对公共数据库中所有基因组和宏基因组蛋白质序列数据的综合分析揭示了不同古细菌和细菌中替代半胱氨酸编码系统的分布和进化。SepRS-SepCysS-SepCysE-和硒代半胱氨酸编码系统由Euryarchaeota I类产甲烷菌、Crenarchaeota AK 8/W8 A-19组和Asgard古菌共享的发现表明，古代古菌可能使用了这两种系统。相比之下，细菌可能已经从古细菌获得了SepRS-SepCysS系统。SepRS-SepCysS系统有时与古细菌和细菌中的吡咯赖氨酸编码系统共存。我们的研究结果为SepRS-SepCysS系统对硫同化和需要大量铁硫酶和蛋白质的多种代谢的贡献提供了额外的生物信息学证据。在这些生物活动中，甲烷生成、甲胺代谢和有机卤化物呼吸可能对地球产生局部和全球影响。总之，未培养的细菌和古生菌提供了遗传密码进化的扩展记录。
The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNACys is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria (“Candidatus Parcubacteria” and Chloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNACys species with cysteine in vitro. Homologs of SepCysE, a scaffold protein facilitating SepRS⋅SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. We discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes. Comprehensive analyses of all genomic and metagenomic protein sequence data in public databases revealed the distribution and evolution of an alternative cysteine-encoding system in diverse archaea and bacteria. The finding that the SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon suggests that ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria. Our results provide additional bioinformatic evidence for the contribution of the SepRS-SepCysS system for sulfur assimilation and diverse metabolisms which require vast amounts of iron-sulfur enzymes and proteins. Among these biological activities, methanogenesis, methylamine metabolism, and organohalide respiration may have local and global effects on earth. Taken together, uncultured bacteria and archaea provide an expanded record of the evolution of the genetic code.