Couto Jillian M, Ijaz Umer Zeeshan, Phoenix Vernon R, Schirmer Melanie, Sloan William T
Division of Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Level 5, Glasgow, G12 8LT, Scotland, UK,
Curr Microbiol. 2015 Aug;71(2):296-302. doi: 10.1007/s00284-015-0846-2. Epub 2015 Jun 5.
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 [1], 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.
许多利用氢化酶的有前景的氢能技术都因大多数氢化酶对氧气极为敏感这一事实而进展缓慢。在第1类膜结合镍铁氢化酶中，确实存在天然的耐受性酶，而氧气耐受性很大程度上归因于该酶小亚基中由不同数量半胱氨酸残基配位的铁硫簇的变化。事实上，先前的研究已经提供了一个关于氧气耐受性的强大系统发育特征[1]，当与新的测序技术相结合时，使得在自然界中进行生物勘探成为一项更可行的努力。然而，理解如此巨大的多样性仍然具有挑战性，如果能为已知的具有氧气耐受性酶的物种标注有关代谢和自然环境的信息，可能会使其得到简化。在这里，我们采用生物信息学方法，比较了来自177个具有全基因组测序的细菌物种的氧气耐受性和敏感性膜结合镍铁氢化酶在分类学、氧气需求和自然环境方面的差异。在此之后，我们使用Illumina™ MiSeq平台通过高通量鸟枪法DNA测序，对湖相表层沉积物的宏基因组进行了新型氢化酶的探寻。我们发现了44个新的镍铁第1类膜结合氢化酶序列片段，其中5个在该酶小亚基的系统发育树上与耐受性组聚类，4个与大亚基聚类，这表明有从头合成的氧气耐受性蛋白质序列，可能有助于设计出更高效的氢化酶。
