第一作者：Jiahui Hu, Ruiyang Li
通讯作者：李炳 副教授
通讯单位：清华大学深圳国际研究生院环境与生态研究所
DOI:10.1016/j.watres.2024.123037
阐明生物降解机制和预测污染物的反应性对于推进生物降解工程的应用以应对成千上万新出现的污染物的挑战至关重要。分子生物学和计算化学是实现这一目标的有力工具，可以在基因和原子水平上研究生化反应。本研究以十种磺胺类抗生素的生物降解为例，展示了基因组学和量子化学方法在探索新兴污染物生物降解行为中的整合。分离得到的功能菌株Paenarthrobacter sp.在好氧条件下可以完全降解所有10种模式磺胺。这些化合物共用一个4-氨基苯磺酰胺核，但在n1取代环上有所不同。尽管结构不同，但所有的磺胺都遵循一致的降解途径，最终产物为胺化杂环。该途径包括脱氢活化、ipso-羟基化和S-N和S-C键的裂解等关键步骤，其中S-N和S-C键尤其受n1取代基的影响。杂环结构通过改变磺胺的C3和N1原子的电子密度来影响生物降解率。具有较高给电子势和较低吉布斯自由能垒的取代基可显著提高S-C和C-N键的生物降解效率。这项工作不仅揭示了磺胺类化合物的普遍生物降解机制，而且为预测新出现的污染物的生物降解行为和模式提供了理论见解。这些发现有助于有效去除水生环境中新出现的污染物，促进生物处理技术的实际应用。
Fig. 1. Genomic and enzymic characterization of Paenarthrobacter sp. Z3. (a) Genome-based phylogenetic tree constructed utilizing concatenated essential proteins. Bootstrap values were supported by 1000 replications; (b) Comparative genomic characterization of Paenarthrobacter sp. Z3. Rings from outside to inside: ring 1, CDS located in sense chain in orange; 2. CDS located in the antisense chain in blue; 3. tRNA in yellow line and rRNA in purple line; 4. GC content proportion in purple; 5. CG offset in green; 6. Sequencing depth in shallow blue; (c) Schematic representations of the binding mode of FMNHOOH (wheat) and SMZ (cyan) in sulfonamide monooxygenase (smudge) of Paenarthrobacter sp. Z3. The binding sites was referred with Kim, et al. 1.
Fig. 2. Biodegradation of sulfonamides by Paenarthrobacter sp. Z3. (a) Degradation kinetics of selected sulfonamides; (b) OD600 of bacteria during the degradation of sulfonamides; (c) Mineralization rate of selected sulfonamides; (d) Removal of SMZ and TOC, as well as OD600 of bacteria in the SMZ biodegradation system.
Fig. 3. The biodegradation of sulfonamides and the effects of sulfonamide species on biodegradation. (a) Biodegradation pathway of sulfonamides and the related functional genes responsible for their biotransformation; (b) Species of sulfonamides in water; (c) The dehydrogenation activation of neutral sulfonamides, take SMZ as an example; (d) The dehydrogenation activation of anionic sulfonamides, take SMZ as an example; (e) The bond length of S-C and S-N bonds during the biodegradation process.
Fig. 4. The impact of N1 substituents on the biodegradation of sulfonamides. (a) Hirshfeld partial charges on reactive atoms N1, S2, C3, and N4 for both neutral and anionic sulfonamides; (b) Free energy diagram for neutral and anionic sulfonamides, with SMZ serving as a representative example; (c) Theoretical calculations of reaction free energy (ΔG) and free energy barrier (ΔG‡) for the S-C and S-N cleavage steps; (d) The linear relationship between the natural logarithm of the maximum biodegradation rate constants (ln transformed) and ΔG‡ for the concerted cleavage processes. The data points for SMX and SRZ, marked in gray, deviate from this linear correlation and are excluded from the regression analysis.
本研究提出了一种结合分子生物学和计算化学的综合方法来探索新兴污染物的生物降解行为。分子生物学鉴定关键基因和酶，而计算化学评估分子结构如何影响反应动力学和降解途径。以磺胺类化合物为例，分析了拟环节杆菌sp. Z3对10种磺胺类化合物的生物降解作用，得到了以下结果：
（1)经鉴定，sadA编码的黄素依赖性单加氧酶是产生胺化杂环的催化酶。
（2)阴离子比中性分子反应性更强，杂环上的供电子取代基通过增加反应原子上的电子密度来促进生物降解。
（3）生物降解过程是热力学和动力学上受S-C和S-N键裂解的自由能垒控制的。
Jiahui Hu, Ruiyang Li, Jiayu Zhang, Lijia Cao, Huaxin Lei, Renxin Zhao, Lin Lin, Xiao-yan Li, Wen Zhang, Bing Li, Deciphering the N1-substituent effects on biodegradation of sulfonamides: Novel insights revealed from molecular biology and computational chemistry approaches, Water Research, 2025, https://doi.org/10.1016/j.watres.2024.123037
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