Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment.
Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment.
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DOI：
10.1007/s00284-015-0846-2
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发表时间：
2015-08
影响因子：
2.6
通讯作者：
Sloan, William T.
中科院分区：
文献类型：
--
作者：
Couto, Jillian M.;Ijaz, Umer Zeeshan;Phoenix, Vernon R.;Schirmer, Melanie;Sloan, William T.
许多利用氢化酶的有前途的氢技术由于大多数氢化酶对O2极其敏感的事实而被减缓。在组1膜结合的NiFe氢化酶，天然存在的耐受酶确实存在，和O2耐受性已在很大程度上归因于铁硫簇的变化协调不同数量的半胱氨酸残基在酶的小亚基。事实上，以前的工作已经提供了一个强大的O2耐受性的系统发育特征，当与新的测序技术相结合时，自然界的生物勘探变得更加可行。然而，理解如此巨大的多样性仍然具有挑战性，如果用代谢和自然环境的信息注释具有O2耐受酶的已知物种，则可以简化。在这里，我们利用生物信息学方法比较了来自177种细菌物种的耐O2和敏感的膜结合NiFe氢化酶，这些细菌具有完全测序的基因组，以了解其分类学、O2需求和自然环境的差异。在此之后，我们通过使用Illumina™ MiSeq平台的高通量鸟枪DNA测序来询问来自湖泊表面沉积物的宏基因组中的新型氢化酶。我们发现了44个新的NiFe组1膜结合氢化酶序列片段，其中5个与酶的小亚基的系统发育树上的耐受组分离，4个与大亚基分离，表明从头O2耐受蛋白质序列，可以帮助工程师更有效的氢化酶。本文的在线版本（doi：10.1007/s 00284 -015-0846-2）包含补充材料，可供授权用户使用。
Many promising hydrogen technologies utilising hydrogenase enzymes have been slowed by the fact that most hydrogenases are extremely sensitive to O2. Within the group 1 membrane-bound NiFe hydrogenase, naturally occurring tolerant enzymes do exist, and O2 tolerance has been largely attributed to changes in iron–sulphur clusters coordinated by different numbers of cysteine residues in the enzyme’s small subunit. Indeed, previous work has provided a robust phylogenetic signature of O2 tolerance, which when combined with new sequencing technologies makes bio prospecting in nature a far more viable endeavour. However, making sense of such a vast diversity is still challenging and could be simplified if known species with O2-tolerant enzymes were annotated with information on metabolism and natural environments. Here, we utilised a bioinformatics approach to compare O2-tolerant and sensitive membrane-bound NiFe hydrogenases from 177 bacterial species with fully sequenced genomes for differences in their taxonomy, O2 requirements, and natural environment. Following this, we interrogated a metagenome from lacustrine surface sediment for novel hydrogenases via high-throughput shotgun DNA sequencing using the Illumina™ MiSeq platform. We found 44 new NiFe group 1 membrane-bound hydrogenase sequence fragments, five of which segregated with the tolerant group on the phylogenetic tree of the enzyme’s small subunit, and four with the large subunit, indicating de novo O2-tolerant protein sequences that could help engineer more efficient hydrogenases. The online version of this article (doi:10.1007/s00284-015-0846-2) contains supplementary material, which is available to authorized users.
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DOI：
10.1099/ijs.0.02636-0
发表时间：
2004-01-01
影响因子：
2.8
作者：
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通讯作者：
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影响因子：
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DOI：
10.1042/bj20131520
发表时间：
2014-03-15
期刊：
The Biochemical journal
影响因子：
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作者：
Bowman L;Flanagan L;Fyfe PK;Parkin A;Hunter WN;Sargent F
通讯作者：
Sargent F