Laboratory of Molecular Microbiology and Biotechnology, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Viale delle Scienze, ed. 16, 90128, Palermo, Italy.
Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
BMC Microbiol. 2018 Nov 27;18(1):198. doi: 10.1186/s12866-018-1330-5.
Klebsiella oxytoca DSM 29614 - isolated from acid mine drainages - grows anaerobically using Fe(III)-citrate as sole carbon and energy source, unlike other enterobacteria and K. oxytoca clinical isolates. The DSM 29614 strain is multi metal resistant and produces metal nanoparticles that are embedded in its very peculiar capsular exopolysaccharide. These metal nanoparticles were effective as antimicrobial and anticancer compounds, chemical catalysts and nano-fertilizers.
The DSM 29614 strain genome was sequenced and analysed by a combination of in silico procedures. Comparative genomics, performed between 85 K. oxytoca representatives and K. oxytoca DSM 29614, revealed that this bacterial group has an open pangenome, characterized by a very small core genome (1009 genes, about 2%), a high fraction of unique (43,808 genes, about 87%) and accessory genes (5559 genes, about 11%). Proteins belonging to COG categories "Carbohydrate transport and metabolism" (G), "Amino acid transport and metabolism" (E), "Coenzyme transport and metabolism" (H), "Inorganic ion transport and metabolism" (P), and "membrane biogenesis-related proteins" (M) are particularly abundant in the predicted proteome of DSM 29614 strain. The results of a protein functional enrichment analysis - based on a previous proteomic analysis - revealed metabolic optimization during Fe(III)-citrate anaerobic utilization. In this growth condition, the observed high levels of Fe(II) may be due to different flavin metal reductases and siderophores as inferred form genome analysis. The presence of genes responsible for the synthesis of exopolysaccharide and for the tolerance to heavy metals was highlighted too. The inferred genomic insights were confirmed by a set of phenotypic tests showing specific metabolic capability in terms of i) Fe and exopolysaccharide production and ii) phosphatase activity involved in precipitation of metal ion-phosphate salts.
The K. oxytoca DSM 29614 unique capabilities of using Fe(III)-citrate as sole carbon and energy source in anaerobiosis and tolerating diverse metals coincides with the presence at the genomic level of specific genes that can support i) energy metabolism optimization, ii) cell protection by the biosynthesis of a peculiar exopolysaccharide armour entrapping metal ions and iii) general and metal-specific detoxifying activities by different proteins and metabolites.
从酸性矿山排水中分离出来的克氏柠檬酸杆菌 DSM 29614 是一种不同于其他肠杆菌和克氏柠檬酸杆菌临床分离株的厌氧菌，它以 Fe(III)-柠檬酸盐为唯一的碳源和能源进行生长。DSM 29614 株具有多金属抗性，并产生嵌入其非常特殊荚膜胞外多糖的金属纳米粒子。这些金属纳米粒子作为抗菌和抗癌化合物、化学催化剂和纳米肥料是有效的。
通过组合使用计算机模拟程序，对 DSM 29614 菌株的基因组进行了测序和分析。对 85 株克氏柠檬酸杆菌代表菌株和克氏柠檬酸杆菌 DSM 29614 进行比较基因组学分析表明，该细菌群具有一个开放的泛基因组，其特征是一个非常小的核心基因组（1009 个基因，约 2%），高比例的独特（43808 个基因，约 87%）和辅助基因（5559 个基因，约 11%）。COG 类别“碳水化合物运输和代谢”（G）、“氨基酸运输和代谢”（E）、“辅酶运输和代谢”（H）、“无机离子运输和代谢”（P）和“膜生物发生相关蛋白”（M）中的蛋白质在 DSM 29614 菌株的预测蛋白质组中特别丰富。基于以前的蛋白质组学分析的蛋白质功能富集分析的结果表明，在 Fe(III)-柠檬酸盐厌氧利用过程中进行了代谢优化。在这种生长条件下，观察到的高水平 Fe(II)可能是由于不同的黄素金属还原酶和铁载体所致，这可以从基因组分析中推断出来。还强调了负责荚膜多糖合成和耐受重金属的基因的存在。一组表型测试证实了推断的基因组见解，这些测试显示了在 Fe 和胞外多糖的产生以及涉及金属离子-磷酸盐盐沉淀的磷酸酶活性方面的特定代谢能力。
克氏柠檬酸杆菌 DSM 29614 在厌氧条件下以 Fe(III)-柠檬酸盐为唯一碳源和能源的独特能力，以及耐受多种金属的能力，与在基因组水平上存在特定基因相吻合，这些基因可以支持 i）能量代谢的优化，ii）通过合成特殊的荚膜多糖盔甲来保护细胞免受金属离子的侵害，iii）通过不同的蛋白质和代谢物进行一般和金属特异性的解毒活性。
