A synthetic biology and green bioprocess approach to recreate agarwood sesquiterpenoid mixtures

Certain endangered Thymelaeaceous trees are major sources of the fragrant and highly valued resinous agarwood, comprised of hundreds of oxygenated sesquiterpenoids (STPs). Despite growing pressure on natural agarwood sources, the chemical complexity of STPs severely limits synthetic production. Here, we catalogued the chemical diversity in 58 agarwood samples by two-dimensional gas chromatography–mass spectrometry and partially recreated complex STP mixtures through synthetic biology. We improved STP yields in the unicellular alga Chlamydomonas reinhardtii by combinatorial engineering to biosynthesise nine macrocyclic STP backbones found in agarwood. A bioprocess following green-chemistry principles was developed that exploits ‘milking’ of STPs without cell lysis, solvent–solvent STP extraction, solvent–STP nanofiltration, and bulk STP oxy-functionalisation to obtain terpene mixtures like those of agarwood. This process occurs with total solvent recycling and enables continuous producti..., Agarwood sample collection and processing
Agarwood samples were procured from the old-town market \"Al Balad\" in Jeddah, Saudi Arabia (21.481° N, 39.187° E) in Winter 2023. The collection includes 36 different samples of agarwood chips, dried Aquilaria spp. wood (also known as \"bahkour\"), and 22 agarwood steam-distillate oils, known as \"oudh\". The ages of the plants at harvest and origins of these samples cannot be accurately traced; however, many were labelled with their country of origin. The samples varied in price at the time of purchase, reflecting their purported rarity, the density of fragrant compounds, and complexity of aromatic notes (Supplementary Table 1). It was determined that the appropriate organic solvent for extraction was acetone based on preliminary analysis with different solvents, and each agarwood sample was then diluted to obtain chromatograms with clear peaks for product detection and identification. All samples were processed within 16 weeks of being procured. T..., , This README file was generated on 2024-01-12 by Sergio Gutiérrez

# General information

## Dataset Title

A Synthetic Biology and Green Bioprocess Approach to Recreate Agarwood Sesquiterpenoid Mixtures

## Date of Data Collection

2022-2023

## Contributors

* Sergio Gutiérrez, Sebastian Overmans, Gordon B. Wellman: Bioengineering Program, BESE Division, KAUST, Thuwal, Saudi Arabia.
* Vasilios G. Samaras: Analytical Chemistry Core Lab (ACL), KAUST, Thuwal, Saudi Arabia.
* Claudia Oviedo: Advanced Membranes and Porous Materials Center (AMPM), PSE Division & Environmental Science and Engineering Program, BESE Division, KAUST, Thuwal, Saudi Arabia.
* Martin Gede: AMPM, PSE Division & Chemical Engineering Program, KAUST, Thuwal, Saudi Arabia.
* Gyorgy Szekely: AMPM, PSE Division, Environmental Science and Engineering Program, BESE Division & Chemical Engineering Program, KAUST, Thuwal, Saudi Arabia.
* Kyle J. Lauersen (Corresponding Author): Bioengineering Program, ...

部分濒危瑞香科（Thymelaeaceae）植物是高香气、高经济价值的树脂状沉香（agarwood）的核心来源，其成分包含数百种含氧倍半萜（oxygenated sesquiterpenoids, STPs）。尽管天然沉香资源正承受日益加剧的开发压力，但含氧倍半萜复杂的化学特性严重制约了其人工合成生产。本研究通过二维气相色谱-质谱联用法（two-dimensional gas chromatography–mass spectrometry）对58份沉香样品的化学多样性进行了系统表征，并通过合成生物学手段部分复刻了复杂的倍半萜混合物。我们通过组合工程改造提升了单细胞藻类莱茵衣藻（Chlamydomonas reinhardtii）的倍半萜产量，使其能够生物合成沉香中存在的9种大环倍半萜骨架。本研究开发了一套遵循绿色化学（green chemistry）原则的生物工艺：通过无细胞裂解的“挤取”策略提取倍半萜，结合溶剂-溶剂萃取、溶剂-倍半萜纳滤及大规模倍半萜氧化官能化技术，获得了与沉香特征相符的萜类混合物。该工艺可实现溶剂完全循环利用，支持连续生产……
## 沉香样品采集与处理
本研究于2023年冬季从沙特阿拉伯吉达市老城区市场Al Balad（坐标：21.481° N, 39.187° E）采购沉香样品。本次采集的样品包括36份沉香木片、干燥沉香属（Aquilaria spp.）木材（又称“bahkour”）样品，以及22份沉香水蒸气蒸馏精油（又称“oudh”）样品。无法精准追溯样品对应植株的采伐树龄与原产地，但多数样品标注了其原产国。采购时样品价格存在差异，这与其宣称的稀有程度、香气化合物含量及香气特征复杂度相符（详见补充表1）。经不同溶剂预实验筛选，确定丙酮为最优萃取溶剂；随后对所有沉香样品进行稀释，以获得峰形清晰的色谱图，用于产物检测与鉴定。所有样品均在采购后16周内完成处理。
本说明文件于2024年1月12日由Sergio Gutiérrez生成。

# 通用信息

## 数据集标题
一种用于复刻沉香倍半萜混合物的合成生物学与绿色生物工艺方法

## 数据采集时间
2022-2023

## 贡献者
* Sergio Gutiérrez, Sebastian Overmans, Gordon B. Wellman：沙特阿拉伯图沃勒阿卜杜拉国王科技大学（KAUST）BESE学部生物工程项目
* Vasilios G. Samaras：沙特阿拉伯图沃勒阿卜杜拉国王科技大学（KAUST）分析化学核心实验室（ACL）
* Claudia Oviedo：沙特阿拉伯图沃勒阿卜杜拉国王科技大学（KAUST）PSE学部先进膜与多孔材料中心（AMPM）及BESE学部环境科学与工程项目
* Martin Gede：沙特阿拉伯图沃勒阿卜杜拉国王科技大学（KAUST）PSE学部先进膜与多孔材料中心（AMPM）及化学工程项目
* Gyorgy Szekely：沙特阿拉伯图沃勒阿卜杜拉国王科技大学（KAUST）PSE学部先进膜与多孔材料中心（AMPM）、BESE学部环境科学与工程项目及化学工程项目
* Kyle J. Lauersen（通讯作者）：沙特阿拉伯图沃勒阿卜杜拉国王科技大学（KAUST）BESE学部生物工程项目