Biome-specific distribution of Ni-containing carbon monoxide dehydrogenases.

IF 2.6 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Masao Inoue, Kimiho Omae, Issei Nakamoto, Ryoma Kamikawa, Takashi Yoshida, Yoshihiko Sako
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引用次数: 5

Abstract

Ni-containing carbon monoxide dehydrogenase (Ni-CODH) plays an important role in the CO/CO2-based carbon and energy metabolism of microbiomes. Ni-CODH is classified into distinct phylogenetic clades, A-G, with possibly distinct cellular roles. However, the types of Ni-CODH clade used by organisms in different microbiomes are unknown. Here, we conducted a metagenomic survey of a protein database to determine the relationship between the phylogeny and biome distribution of Ni-CODHs. Clustering and phylogenetic analyses showed that the metagenome assembly-derived Ni-CODH sequences were distributed in ~ 60% Ni-CODH clusters and in all Ni-CODH clades. We also identified a novel Ni-CODH clade, clade H. Biome mapping on the Ni-CODH phylogenetic tree revealed that Ni-CODHs of almost all the clades were found in natural aquatic environmental and engineered samples, whereas those of specific subclades were found only in host-associated samples. These results are comparable with our finding that the diversity in the phylum-level taxonomy of host-associated Ni-CODH owners is statistically different from those of the other biomes. Our findings suggest that while Ni-CODH is a ubiquitous enzyme produced across diverse microbiomes, its distribution in each clade is biased and mainly affected by the distinct composition of microbiomes.

Abstract Image

Abstract Image

Abstract Image

含镍一氧化碳脱氢酶的生物群系特异性分布。
含镍一氧化碳脱氢酶(Ni-CODH)在微生物组CO/ co2基碳和能量代谢中起着重要作用。Ni-CODH被划分为不同的系统发育分支,A-G,可能具有不同的细胞作用。然而,不同微生物组中生物使用的Ni-CODH分支的类型尚不清楚。在此,我们对一个蛋白质数据库进行了宏基因组调查,以确定Ni-CODHs的系统发育与生物群落分布之间的关系。聚类和系统发育分析表明,元基因组组装衍生的Ni-CODH序列分布在约60%的Ni-CODH集群和所有Ni-CODH支系中。我们还发现了一个新的Ni-CODH进化枝,进化枝H.在Ni-CODH系统发育树上的生物组图谱显示,几乎所有进化枝的Ni-CODH都存在于天然水生环境和工程样品中,而特定亚进化枝的Ni-CODH仅存在于宿主相关样品中。这些结果与我们的发现相当,即宿主相关的Ni-CODH所有者的门级分类多样性与其他生物群系的多样性在统计学上存在差异。我们的研究结果表明,虽然Ni-CODH是一种在不同微生物组中产生的普遍存在的酶,但其在每个进化支中的分布是有偏差的,主要受微生物组不同组成的影响。
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来源期刊
Extremophiles
Extremophiles 生物-生化与分子生物学
CiteScore
6.80
自引率
6.90%
发文量
28
审稿时长
2 months
期刊介绍: Extremophiles features original research articles, reviews, and method papers on the biology, molecular biology, structure, function, and applications of microbial life at high or low temperature, pressure, acidity, alkalinity, salinity, or desiccation; or in the presence of organic solvents, heavy metals, normally toxic substances, or radiation.
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