Quasem Ishtiaque, Achille Alexandra N, Caddick Brittany A, Carter Travis A, Daniels Camille, Delaney Jennifer A, Delic Vedad, Denton Kimberly A, Duran Martina C, Fatica Marianne K, Ference Christopher M, Galkiewicz Julie P, Garcia Ana M, Hendrick Jacqueline D, Horton Steven A, Kun Mey S, Koch Phoebe W, Lee Tien Min, McCabe Christie R, McHale Sean, McDaniel Lauren D, Menning Damian M, Menning Kristy J, Mirzaei-Souderjani Hamed, Mostajabian Salina, Nicholson David A, Nugent Courtney K, Osman Nicholas P, Pappas Desiree I, Rocha Andrea M, Rosario Karyna, Rubelmann Haydn, Schwartz Julie A, Seeley Kent W, Staley Christopher M, Wallace Elizabeth M, Wong Terianne M, Zielinski Brian L, Hanson Thomas E, Scott Kathleen M
Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA.
School of Marine Science and Policy, Delaware Biotechnology Institute, and Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA.
FEMS Microbiol Lett. 2017 Aug 1;364(14). doi: 10.1093/femsle/fnx148.
The genome sequence of the obligate chemolithoautotroph Hydrogenovibrio crunogenus paradoxically predicts a complete oxidative citric acid cycle (CAC). This prediction was tested by multiple approaches including whole cell carbon assimilation to verify obligate autotrophy, phylogenetic analysis of CAC enzyme sequences and enzyme assays. Hydrogenovibrio crunogenus did not assimilate any of the organic compounds provided (acetate, succinate, glucose, yeast extract, tryptone). Enzyme activities confirmed that its CAC is mostly uncoupled from the NADH pool. 2-Oxoglutarate:ferredoxin oxidoreductase activity is absent, though pyruvate:ferredoxin oxidoreductase is present, indicating that sequence-based predictions of substrate for this oxidoreductase were incorrect, and that H. crunogenus may have an incomplete CAC. Though the H. crunogenus CAC genes encode uncommon enzymes, the taxonomic distribution of their top matches suggests that they were not horizontally acquired. Comparison of H. crunogenus CAC genes to those present in other 'Proteobacteria' reveals that H. crunogenus and other obligate autotrophs lack the functional redundancy for the steps of the CAC typical for facultative autotrophs and heterotrophs, providing another possible mechanism for obligate autotrophy.
专性化能自养菌嗜压氢弧菌（Hydrogenovibrio crunogenus）的基因组序列反常地预测其具有完整的氧化型柠檬酸循环（CAC）。通过多种方法对这一预测进行了验证，包括全细胞碳同化以确认专性自养特性、对CAC酶序列进行系统发育分析以及酶活性测定。嗜压氢弧菌不能同化所提供的任何有机化合物（乙酸盐、琥珀酸盐、葡萄糖、酵母提取物、胰蛋白胨）。酶活性证实其柠檬酸循环大多与NADH库解偶联。虽然存在丙酮酸：铁氧化还原蛋白氧化还原酶，但不存在2-氧代戊二酸：铁氧化还原蛋白氧化还原酶活性，这表明基于序列对该氧化还原酶底物的预测是错误的，并且嗜压氢弧菌可能具有不完整的柠檬酸循环。尽管嗜压氢弧菌的柠檬酸循环基因编码不常见的酶，但其最佳匹配序列的分类分布表明它们并非通过水平基因转移获得。将嗜压氢弧菌的柠檬酸循环基因与其他“变形菌门”细菌中的基因进行比较发现，嗜压氢弧菌和其他专性自养菌在兼性自养菌和异养菌典型的柠檬酸循环步骤中缺乏功能冗余，这为专性自养提供了另一种可能的机制。
