Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates.
Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates.
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DOI：
10.3389/fmicb.2016.00100
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发表时间：
2016
影响因子：
5.2
通讯作者：
Edwards EA
中科院分区：
文献类型：
--
作者：
Tang S;Wang PH;Higgins SA;Löffler FE;Edwards EA
从厌氧富集培养物的宏基因组中组装了两种密切相关的脱卤菌菌株（菌株CF和菌株DCA）的基因组，所述厌氧富集培养物还原性地脱氯氯仿（CF）、1，1，1-三氯乙烷（1，1，1-TCA）和1，1-二氯乙烷（1，1-DCA）。菌株CF（使CF和1，1，1-TCA脱氯）和菌株DCA（使1，1-DCA脱氯）的3.1Mbp基因组各自含有17个推定的还原脱卤酶同源（rdh）基因。将这两个基因组与其他三种可用的呼吸有机卤化物的脱卤杆菌基因组（限制性脱卤杆菌菌株PER-K23、脱卤杆菌属菌株E1和脱卤杆菌属菌株UNSWDHB）以及Dehalococcoides mccartyi菌株195和Desulfitobacterium hafniense菌株Y51的基因组进行了系统性比较。该分析比较了42种不同的代谢和生理类别。菌株CF和DCA的基因组在排除大插入的2.9 Mbp比对中共有90%的总体平均核苷酸同一性和>99.8%的同一性，表明这些基因组从接近的共同祖先分化而来。这种分化可能是由两个邻位还原脱卤酶基因cfrA和dcrA周围的选择压力驱动的，这两个基因编码还原CF或1，1，1-TCA和1，1-DCA的酶。在五个脱卤酶基因组中发现的许多还原性脱卤酶基因聚簇成两个小的保守区域，并且通常与Crp/Fnr转录调节因子相关。特化是在菌株特异性的基础上进行的，因为一些菌株而不是其他菌株在Wood-Ljungdahl（菌株E1）和corrinoid生物合成途径（菌株E1和PER-K23）中丢失了必需基因。编码磷酸丝氨酸磷酸酶的基因，催化丝氨酸生物合成的最后一步，在所有五个脱卤虫基因组中缺失，但D。restrictus可以在没有丝氨酸的情况下生长，这表明存在替代的或未被识别的生物合成途径。与D. mccartyi，一个完整的血红素生物合成途径存在于五个脱卤酶基因组中。这一途径对应于一个新描述的替代血红素生物合成途径，首先确定在pestea。这种有机卤化物呼吸厚壁菌门和Chloroflexi的分析揭示了深刻的进化差异，尽管非常相似的生态位特异性代谢和功能。
The genomes of two closely related Dehalobacter strains (strain CF and strain DCA) were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA). The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA) and strain DCA (that dechlorinates 1,1-DCA) each contain 17 putative reductive dehalogenase homologous (rdh) genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB), and to the genomes of Dehalococcoides mccartyi strain 195 and Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and >99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1) and corrinoid biosynthesis pathways (strains E1 and PER-K23). The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to D. mccartyi, a complete heme biosynthesis pathway is present in the five Dehalobacter genomes. This pathway corresponds to a newly described alternative heme biosynthesis route first identified in Archaea. This analysis of organohalide-respiring Firmicutes and Chloroflexi reveals profound evolutionary differences despite very similar niche-specific metabolism and function.