Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.
Cell Rep. 2023 Aug 29;42(8):112847. doi: 10.1016/j.celrep.2023.112847. Epub 2023 Jul 28.
Bioconversion of lignin-related aromatic compounds relies on robust catabolic pathways in microbes. Sphingobium sp. SYK-6 (SYK-6) is a well-characterized aromatic catabolic organism that has served as a model for microbial lignin conversion, and its utility as a biocatalyst could potentially be further improved by genome-wide metabolic analyses. To this end, we generate a randomly barcoded transposon insertion mutant (RB-TnSeq) library to study gene function in SYK-6. The library is enriched under dozens of enrichment conditions to quantify gene fitness. Several known aromatic catabolic pathways are confirmed, and RB-TnSeq affords additional detail on the genome-wide effects of each enrichment condition. Selected genes are further examined in SYK-6 or Pseudomonas putida KT2440, leading to the identification of new gene functions. The findings from this study further elucidate the metabolism of SYK-6, while also providing targets for future metabolic engineering in this organism or other hosts for the biological valorization of lignin.
木质素相关芳香族化合物的生物转化依赖于微生物中强大的分解代谢途径。鞘氨醇单胞菌 sp. SYK-6（SYK-6）是一种经过充分研究的芳香族分解代谢生物，它被用作微生物木质素转化的模型，通过全基因组代谢分析，其作为生物催化剂的用途可能会进一步得到改善。为此，我们生成了一个随机条形码转座子插入突变体（RB-TnSeq）文库，以研究 SYK-6 中的基因功能。该文库在数十种富集条件下进行富集，以量化基因适应性。确认了几个已知的芳香族分解代谢途径，RB-TnSeq 还提供了每个富集条件对全基因组影响的更多细节。选择的基因在 SYK-6 或恶臭假单胞菌 KT2440 中进一步进行了研究，从而确定了新的基因功能。这项研究的结果进一步阐明了 SYK-6 的代谢，同时也为该生物或其他宿主的木质素生物价值化的未来代谢工程提供了目标。
