Genomic analysis of Calderihabitans maritimus KKC1, a thermophilic hydrogenogenic carboxydotrophic bacterium isolated from marine sediment.
Genomic analysis of Calderihabitans maritimus KKC1, a thermophilic hydrogenogenic carboxydotrophic bacterium isolated from marine sediment.
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Calderihabitans maritimus KKC1（一种从海洋沉积物中分离出来的嗜热产氢一氧化碳营养细菌）的基因组分析。
DOI：
10.1128/aem.00832-17
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发表时间：
2017
期刊：
影响因子：
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通讯作者：
Takashi Yoshida and Yoshihiko Sako
中科院分区：
文献类型：
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作者：
Kimiho Omae;Yasuko Yoneda;Yuto Fukuyama;Takashi Yoshida and Yoshihiko Sako
Calderihabitans maritimus KKC 1是一种产氢的嗜热一氧化碳营养菌，分离自水下破火山口。在此，我们描述了C. maritimus KKC 1基因组。基于基因组的系统发育分析证实C. maritimus KKC 1与Moorella属关系最密切，Moorella属包括研究充分的产乙酸成员。比较基因组分析表明，与Moorella、C. maritimus KKC 1保留了CO2还原Wood-Ljungdahl途径和由还原铁氧还蛋白激活的能量转化氢化酶模块，但缺乏HydABC和NfnAB电子分支酶以及丙酮酸：铁氧还蛋白氧化还原酶，这些酶是产乙酸生长所需的铁氧还蛋白还原酶。此外，C. maritimus KKC 1具有6个编码CooS的基因，CooS是厌氧CO脱氢酶的催化亚基，可以通过CO氧化还原铁氧还蛋白，而Moorella只有2个CooS基因。我们的分析表明，在其他微生物中，三个生态基因形成了已知的基因簇，即，cooS-乙酰辅酶A（acetyl-CoA）合酶（含有移码突变）、cooS-能量转换氢化酶和cooF-cooS-FAD-NAD氧化还原酶，而其他三个具有新的基因组背景。序列组成分析表明，这些EcoS基因可能是从一个共同的祖先进化而来的。这些数据表明，C. maritimus KKC 1可能是高度依赖于CO作为一个低电位的电子供体，直接减少铁氧还蛋白，并可能更适合于一氧化碳营养的增长相比，在Moorella中观察到的产乙酸的增长，这表明适应在热力学limit. IMPORTANCEalderihabitans maritimus KKC 1和成员的属Moorella是遗传相关的，但生理上不同。前者是一种产氢的一氧化碳营养菌，可以在一氧化碳（CO）上生长并产生H2，而后者包括产乙酸的细菌，可以在H2 + CO2上生长并产生乙酸。这两种物质可能都需要还原的铁氧还蛋白作为实际的“能量当量”，但铁氧还蛋白是一种低电位的电子载体，需要高能底物作为还原的电子供体。比较基因组分析表明，C. maritimus KKC 1缺乏特定的电子分支酶，并拥有6个CO脱氢酶，不像Moorella物种。这表明C.海栖穆尔氏菌KKC 1可能更依赖于CO，这是一种强电子供体，可以通过CO脱氢酶直接还原铁氧还蛋白，并且可能表现出与产乙酸穆尔氏菌不同的生存策略，其解决了与用氢内吸还原铁氧还蛋白相关的能量障碍。
Calderihabitans maritimus KKC1 is a thermophilic, hydrogenogenic carboxydotroph isolated from a submerged marine caldera. Here, we describe thede novosequencing and feature analysis of the C. maritimus KKC1 genome. Genome-based phylogenetic analysis confirmed that C. maritimus KKC1 was most closely related to the genus Moorella, which includes well-studied acetogenic members. Comparative genomic analysis revealed that, like Moorella, C. maritimus KKC1 retained both the CO2-reducing Wood-Ljungdahl pathway and energy-converting hydrogenase-based module activated by reduced ferredoxin, but it lacked the HydABC and NfnAB electron-bifurcating enzymes and pyruvate:ferredoxin oxidoreductase required for ferredoxin reduction for acetogenic growth. Furthermore, C. maritimus KKC1 harbored six genes encoding CooS, a catalytic subunit of the anaerobic CO dehydrogenase that can reduce ferredoxin via CO oxidation, whereas Moorella possessed only two CooS genes. Our analysis revealed that threecooSgenes formed known gene clusters in other microorganisms, i.e.,cooS-acetyl coenzyme A (acetyl-CoA) synthase (which contained a frameshift mutation),cooS–energy-converting hydrogenase, andcooF-cooS-FAD-NAD oxidoreductase, while the other three had novel genomic contexts. Sequence composition analysis indicated that thesecooSgenes likely evolved from a common ancestor. Collectively, these data suggest that C. maritimus KKC1 may be highly dependent on CO as a low-potential electron donor to directly reduce ferredoxin and may be more suited to carboxydotrophic growth compared to the acetogenic growth observed in Moorella, which show adaptation at a thermodynamic limit.IMPORTANCECalderihabitans maritimus KKC1 and members of the genus Moorella are phylogenetically related but physiologically distinct. The former is a hydrogenogenic carboxydotroph that can grow on carbon monoxide (CO) with H2production, whereas the latter include acetogenic bacteria that grow on H2plus CO2with acetate production. Both species may require reduced ferredoxin as an actual “energy equivalent,” but ferredoxin is a low-potential electron carrier and requires a high-energy substrate as an electron donor for reduction. Comparative genomic analysis revealed that C. maritimus KKC1 lacked specific electron-bifurcating enzymes and possessed six CO dehydrogenases, unlike Moorella species. This suggests that C. maritimus KKC1 may be more dependent on CO, a strong electron donor that can directly reduce ferredoxin via CO dehydrogenase, and may exhibit a survival strategy different from that of acetogenic Moorella, which solves the energetic barrier associated with endergonic reduction of ferredoxin with hydrogen.