Elcheninov Alexander G, Ugolkov Yaroslav A, Elizarov Ivan M, Klyukina Alexandra A, Kublanov Ilya V, Sorokin Dimitry Y
Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.
Department of Biotechnology, Delft University of Technology, Delft, Netherlands.
Front Microbiol. 2023 Jun 1;14:1112247. doi: 10.3389/fmicb.2023.1112247. eCollection 2023.
Extremely halophilic archaea are one of the principal microbial community components in hypersaline environments. The majority of cultivated haloarchaea are aerobic heterotrophs using peptides or simple sugars as carbon and energy sources. At the same time, a number of novel metabolic capacities of these extremophiles were discovered recently among which is a capability of growing on insoluble polysaccharides such as cellulose and chitin. Still, polysaccharidolytic strains are in minority among cultivated haloarchaea and their capacities of hydrolyzing recalcitrant polysaccharides are hardly investigated. This includes the mechanisms and enzymes involved in cellulose degradation, which are well studied for bacterial species, while almost unexplored in archaea and haloarchaea in particular. To fill this gap, a comparative genomic analysis of 155 cultivated representatives of halo(natrono)archaea, including seven cellulotrophic strains belonging to the genera , , , and was performed. The analysis revealed a number of cellulases, encoded in the genomes of cellulotrophic strains but also in several haloarchaea, for which the capacity to grow on cellulose was not shown. Surprisingly, the cellulases genes, especially of GH5, GH9 and GH12 families, were significantly overrepresented in the cellulotrophic haloarchaea genomes in comparison with other cellulotrophic archaea and even cellulotrophic bacteria. Besides cellulases, the genes for GH10 and GH51 families were also abundant in the genomes of cellulotrophic haloarchaea. These results allowed to propose the genomic patterns, determining the capability of haloarchaea to grow on cellulose. The patterns helped to predict cellulotrophic capacity for several halo(natrono)archaea, and for three of them it was experimentally confirmed. Further genomic search revealed that glucose and cellooligosaccharides import occurred by means of porters and ABC (ATP-binding cassette) transporters. Intracellular glucose oxidation occurred through glycolysis or the semi-phosphorylative Entner-Dudoroff pathway which occurrence was strain-specific. Comparative analysis of CAZymes toolbox and available cultivation-based information allowed proposing two possible strategies used by haloarchaea capable of growing on cellulose: so-called specialists are more effective in degradation of cellulose while generalists are more flexible in nutrient spectra. Besides CAZymes profiles the groups differed in genome sizes, as well as in variability of mechanisms of import and central metabolism of sugars.
极端嗜盐古菌是高盐环境中主要的微生物群落组成部分之一。大多数已培养的嗜盐古菌是需氧异养菌，利用肽或单糖作为碳源和能源。与此同时，最近发现了这些嗜极端微生物的一些新的代谢能力，其中包括能够利用不溶性多糖（如纤维素和几丁质）生长的能力。然而，在已培养的嗜盐古菌中，多糖分解菌株占少数，它们水解难降解多糖的能力几乎未得到研究。这包括参与纤维素降解的机制和酶，这些在细菌物种中已有深入研究，而在古菌尤其是嗜盐古菌中几乎未被探索。为了填补这一空白，对155株已培养的嗜盐（嗜钠）古菌代表菌株进行了比较基因组分析，其中包括7株属于、、、和属的纤维素分解菌株。分析揭示了一些纤维素酶，它们不仅在纤维素分解菌株的基因组中编码，在一些未表现出利用纤维素生长能力的嗜盐古菌基因组中也有编码。令人惊讶的是，与其他纤维素分解古菌甚至纤维素分解细菌相比，纤维素酶基因，尤其是GH5、GH9和GH12家族的基因，在纤维素分解嗜盐古菌基因组中显著富集。除了纤维素酶，GH10和GH51家族的基因在纤维素分解嗜盐古菌基因组中也很丰富。这些结果有助于提出基因组模式，确定嗜盐古菌利用纤维素生长的能力。这些模式有助于预测几种嗜盐（嗜钠）古菌的纤维素分解能力，其中三种已通过实验得到证实。进一步的基因组搜索发现，葡萄糖和纤维二糖的转运是通过转运蛋白和ABC（ATP结合盒）转运体进行的。细胞内葡萄糖氧化通过糖酵解或半磷酸化的Entner-Dudoroff途径进行，其发生具有菌株特异性。对碳水化合物活性酶工具箱和现有基于培养的信息进行比较分析，有助于提出嗜盐古菌利用纤维素生长可能采用的两种策略：所谓的“专家型”在纤维素降解方面更有效，而“通用型”在营养谱方面更灵活。除了碳水化合物活性酶谱外，这两类菌株在基因组大小以及糖类转运和中心代谢机制的变异性方面也存在差异。
