Department of Microbiology, University of Massachusetts Amherst Amherst, MA, USA.
Front Microbiol. 2013 Sep 19;4:280. doi: 10.3389/fmicb.2013.00280. eCollection 2013.
Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.
木质纤维素生物燃料作为可持续的替代燃料具有广阔的前景，但木质素抑制了纤维素酶的接触，而木质素降解的副产物可能对细胞有毒。热带土壤细菌进行的厌氧凋落物分解中所使用的酶具有快速生长、高效和特异性，这使得这些生物体成为提高生物燃料生产的有用模板。兼性厌氧菌 Enterobacter lignolyticus SCF1 最初是根据其在木质素作为唯一碳源的条件下进行厌氧生长，从波多黎各的卢奎洛实验林的云雾林土壤中分离出来的。该分离物的来源是快速分解凋落物的热带森林土壤，其氧化还原电位低且波动大，在这种环境中，使用无需氧气的酶的细菌可能在分解中发挥重要作用。我们使用转录组学和蛋白质组学来研究观察到的 SCF1 在添加木质素的培养基中生长时与未添加时相比，生长速度加快的现象。蛋白质组学表明，在木质素添加生长条件下，木糖的摄取和代谢加速，与木质素降解途径（通过 4- 羟基苯乙酸降解途径）、过氧化氢酶/过氧化物酶、谷胱甘肽生物合成和谷胱甘肽 S- 转移酶（GST）蛋白有关的蛋白质上调。我们还观察到 NADH-醌氧化还原酶、其他电子传递链蛋白以及 ATP 合酶和 ATP 结合盒（ABC）转运蛋白的产量增加。这表明木质素被用作末端电子受体。我们随着时间的推移通过吸光度检测到明显的木质素降解，并且还使用代谢组学来证明在木质素添加生长条件下与未添加时相比，木糖浓度显著降低，代谢产物乙酸盐和甲酸盐增加。我们的数据表明，多组学方法具有优势，可以深入了解在自然条件下，微生物如何应对贫碳环境而利用木质素。
