Mechanistic Enzymology of Bacterial Lignin Degradation

细菌木质素降解的机理酶学

• 批准号: BB/M003523/1
• 负责人: Timothy Bugg
• 金额: $ 68.37万
• 依托单位: University of Warwick
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM003523%2F1
• 关键词: Mechanistic; Enzymology; Bacterial; Lignin; Degradation

The chemicals that are used to make plastics, drugs, household chemicals & industrial solvents come primarily from oil, so one of the greatest scientific challenges for the 21st century is how we can find renewable sources for these important chemicals. One obvious place to look is plant lignocellulose, the major component of plant cell walls, found in biomass such as agricultural waste. One component of plant lignocellulose is lignin: an aromatic polymer that is naturally hard to break down, since it is held together by C-O ether linkages and C-C bonds that are not broken down by acid or base treatment. We have isolated bacteria from soil that are able to break down lignin, we have studied in detail the first bacterial lignin-degrading enzyme, an enzyme called peroxidase DypB from Rhodococcus jostii RHA1, and we are beginning to understand the biochemical pathways used by bacteria to break down lignin.We have recently identified a second type of enzyme that can break down lignin,a manganese-dependent superoxide dismutase from Sphingobacterium sp. T2, This is the first time that an enzyme of this kind has been shown to have activity towards lignin. We wish to study in detail the reaction mechanism of this enzyme, to determine exactly what is the reactive species that is responsible for attacking lignin. We have also found another bacterial dyp peroxidase from Pseudomonas fluorescens that can attack lignin, and so we wish to determine the structure of the product that it releases, and determine the mechanism of this reaction. We have also recently determined the three-dimensional structure of a Dyp peroxidase enzyme from Thermobifida fusca; we wish to use this structure to carry out "directed evolution" on this enzyme, to improve its activity towards lignin.We believe that, as well as the lignin-oxidising enzymes such as Dyp peroxidases and Mn superoxide dismutase, there must be other accessory enzymes and proteins that are needed for bacterial lignin breakdown. In this project, we will try to identify an esterase enzyme that breaks an ester linkage between lignin and hemi-cellulose; and a dehydrogenase enzyme that assists lignin breakdown by quenching radical intermediates generated during lignin breakdown. We will then test combinations of these accessory enzymes and lignin-degrading enzymes with samples of lignin either from plant biomass, or from industrial sources, to test whether they are effective for lignin breakdown in vitro, and whether we can use these enzymes to produce aromatic chemicals.

用于制造塑料、药物、家用化学品和工业溶剂的化学品主要来自石油，因此21世纪最大的科学挑战之一是如何为这些重要的化学品找到可再生资源。一个明显的地方是植物木质纤维素，植物细胞壁的主要成分，在农业废物等生物质中发现。植物木质纤维素的一种组分是木质素：一种天然难以分解的芳香族聚合物，因为它通过不被酸或碱处理分解的C-O醚键和C-C键保持在一起。我们已经从土壤中分离出能够分解木质素的细菌，我们已经详细研究了第一种细菌木质素降解酶，一种来自Rhodococcus jostii RHA 1的称为过氧化物酶DypB的酶，我们开始了解细菌分解木质素的生化途径。我们最近发现了第二种可以分解木质素的酶，一种来自鞘氨醇杆菌属T2的锰依赖性超氧化物歧化酶，这是第一次证明这种酶对木质素具有活性。我们希望详细研究这种酶的反应机制，以确定究竟是什么反应物种负责攻击木质素。我们还发现了另一种来自荧光假单胞菌的细菌dyp过氧化物酶，它可以攻击木质素，因此我们希望确定它释放的产物的结构，并确定这种反应的机制。我们最近还确定了来自Thermobifida fusca的Dyp过氧化物酶的三维结构;我们希望利用这种结构对这种酶进行“定向进化”，以提高其对木质素的活性。我们认为，除了木质素氧化酶如Dyp过氧化物酶和Mn超氧化物歧化酶之外，还必须有其他辅助酶和蛋白质才能使细菌木质素分解。在这个项目中，我们将试图确定一种酯酶，打破木质素和半纤维素之间的酯键;和脱氢酶，通过淬灭在木质素分解过程中产生的自由基中间体，帮助木质素分解。然后，我们将测试这些辅助酶和木质素降解酶与来自植物生物质或工业来源的木质素样品的组合，以测试它们是否有效地在体外分解木质素，以及我们是否可以使用这些酶来生产芳香族化学品。

项目成果

A single sensor controls large variations in zinc quotas in a marine cyanobacterium.

• DOI: 10.1038/s41589-022-01051-1
• 发表时间: 2022-08
• 期刊: Nature chemical biology
• 影响因子: 14.8
• 作者: Mikhaylina A;Ksibe AZ;Wilkinson RC;Smith D;Marks E;Coverdale JPC;Fülöp V;Scanlan DJ;Blindauer CA
• 通讯作者: Blindauer CA

Extracellular alpha/beta-hydrolase from Paenibacillus species shares structural and functional homology to tobacco salicylic acid binding protein 2.

来自类芽孢杆菌属物种的胞外 α/β-水解酶与烟草水杨酸结合蛋白 2 具有结构和功能同源性。

• DOI: 10.1016/j.jsb.2020.107496
• 发表时间: 2020
• 期刊: Journal of structural biology
• 影响因子: 3
• 作者: Wilkinson RC

Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes from Rhodococcus jostii RHA1 and Pseudomonas fluorescens Pf-5 Involved in Degradation of Aryl C2 Lignin Degradation Fragments.

红球菌 jostii RHA1 和荧光假单胞菌 Pf-5 参与芳基 C2 木质素降解片段降解的硫胺素二磷酸依赖性 4-羟基苯甲酰甲酸脱羧酶的表征。

• DOI: 10.1021/acs.biochem.9b00177
• 发表时间: 2019
• 期刊: Biochemistry
• 影响因子: 2.9
• 作者: Wei Z

Identification of Manganese Superoxide Dismutase from Sphingobacterium sp. T2 as a Novel Bacterial Enzyme for Lignin Oxidation.

• DOI: 10.1021/acschembio.5b00298
• 发表时间: 2015-08
• 期刊: ACS chemical biology
• 影响因子: 4
• 作者: G. M. Rashid;Charles R. Taylor;Yangqingxue Liu;Xiaoyang Zhang;D. Rea;V. Fülöp;T. Bugg

Sphingobacterium sp. T2 Manganese Superoxide Dismutase Catalyzes the Oxidative Demethylation of Polymeric Lignin via Generation of Hydroxyl Radical.

• DOI: 10.1021/acschembio.8b00557
• 发表时间: 2018-09
• 期刊: ACS chemical biology
• 影响因子: 4
• 作者: G. M. Rashid;Xiaoyang Zhang;R. Wilkinson;V. Fülöp;B. Cottyn;S. Baumberger;T. Bugg