D-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species
D-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species
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DOI：
10.1128/jb.00608-19
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发表时间：
2020-02-01
影响因子：
3.2
通讯作者：
Schoenheit, Peter
中科院分区：
文献类型：
--
作者：
Johnsen, Ulrike;Sutter, Jan-Moritz;Schoenheit, Peter
发现 Haloarcula 物种 H. marismortui 和 H. hispanica 在 D-核糖、D-木糖和 L-阿拉伯糖上生长。在这里，我们报告基于基因组分析、酶的鉴定和表征、转录分析以及敲除突变体的生长实验，发现了一种新的戊糖降解的混杂氧化途径。总之，数据表明，在 Haloarcula spp. 中，D-核糖、D-木糖和 L-阿拉伯糖被降解为 α-酮戊二酸，涉及以下酶：（i）催化 D-核糖、D-木糖和 L-阿拉伯糖氧化的混杂戊糖脱氢酶； (ii) 参与核糖内酯、木糖内酯和阿拉伯内酯水解的混杂戊内酯酶； (iii)高度特异性的脱水酶，核糖酸脱水酶，其催化核糖酸的脱水，以及第二种酶，混杂的木糖酸/葡萄糖酸脱水酶，其参与木糖酸、阿拉伯酸和葡萄糖酸的转化。系统发育分析表明，高度特异性的核糖酸脱水酶构成了烯醇酶超家族中的一个新的糖酸脱水酶家族。 (iv)最后，2-酮-3-脱氧戊酸脱水酶和α-酮戊二酸半醛脱氢酶催化2-酮-3-脱氧戊酸通过α-酮戊二酸半醛转化为α-酮戊二酸。我们得出的结论是，戊糖脱氢酶和戊内酯酶分别对 D-核糖和核糖内酯的底物特异性扩大，以及高度特异性核糖酸脱水酶的存在是 Haloarcula spp 中 D-核糖氧化降解的先决条件。这是古细菌中 D-核糖氧化降解为 α-酮戊二酸途径的首次表征。 重要性 迄今为止，古细菌（生命的第三个领域）中 D-核糖的利用和降解尚未得到分析。我们表明，Haloarcula 物种利用邻核糖，该核糖通过一种新的氧化途径降解为α-酮戊二酸。有证据表明，D-核糖的氧化降解涉及新型混杂酶、戊糖脱氢酶和戊内酯酶，以及对核糖酸高度特异性的新型糖酸脱水酶。这是古细菌中 D-核糖氧化降解途径的首次报道，该途径不同于大多数细菌报道的 D-核糖降解的典型非氧化途径。这些数据有助于我们了解古细菌中不寻常的糖降解途径和酶。
The Haloarcula species H. marismortui and H. hispanica were found to grow on D-ribose, D-xylose, and L-arabinose. Here, we report the discovery of a novel promiscuous oxidative pathway of pentose degradation based on genome analysis, identification and characterization of enzymes, transcriptional analysis, and growth experiments with knockout mutants. Together, the data indicate that in Haloarcula spp., D-ribose, D-xylose, and L-arabinose were degraded to alpha-ketoglutarate involving the following enzymes: (i) a promiscuous pentose dehydrogenase that catalyzed the oxidation of D-ribose, D-xylose, and L-arabinose; (ii) a promiscuous pentonolactonase that was involved in the hydrolysis of ribonolactone, xylonolactone, and arabinolactone; (iii) a highly specific dehydratase, ribonate dehydratase, which catalyzed the dehydration of ribonate, and a second enzyme, a promiscuous xylonate/gluconate dehydratase, which was involved in the conversion of xylonate, arabinonate, and gluconate. Phylogenetic analysis indicated that the highly specific ribonate dehydratase constitutes a novel sugar acid dehydratase family within the enolase superfamily; and (iv) finally, 2-keto-3-deoxypentanonate dehydratase and alpha-ketoglutarate semialdehyde dehydrogenase catalyzed the conversion of 2-keto-3-deoxypentanonate to alpha-ketoglutarate via alpha-ketoglutarate semialdehyde. We conclude that the expanded substrate specificities of the pentose dehydrogenase and pentonolactonase toward D-ribose and ribonolactone, respectively, and the presence of a highly specific ribonate dehydratase are prerequisites of the oxidative degradation of D-ribose in Haloarcula spp. This is the first characterization of an oxidative degradation pathway of D-ribose to alpha-ketoglutarate in archaea.IMPORTANCE The utilization and degradation of D-ribose in archaea, the third domain of life, have not been analyzed so far. We show that Haloarcula species utilize o-ribose, which is degraded to alpha-ketoglutarate via a novel oxidative pathway. Evidence is presented that the oxidative degradation of D-ribose involves novel promiscuous enzymes, pentose dehydrogenase and pentonolactonase, and a novel sugar acid dehydratase highly specific for ribonate. This is the first report of an oxidative degradation pathway of D-ribose in archaea, which differs from the canonical nonoxidative pathway of D-ribose degradation reported for most bacteria. The data contribute to our understanding of the unusual sugar degradation pathways and enzymes in archaea.