Unraveling a novel mechanism for cellulose decomposition in the bacterial phylum Fibrobacteres.

揭示纤维杆菌门中纤维素分解的新机制。

• 批准号: BB/L002043/1
• 负责人: James McDonald
• 金额: $ 41.03万
• 依托单位: Bangor University
• 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%2FL002043%2F1
• 关键词: Unraveling; novel; mechanism; cellulose; decomposition

Cellulose is the most abundant organic polysaccharide on Earth and represents a major structural component of plant cell walls. Consequently, lignocellulosic plant biomass is largely recalcitrant to decomposition by microorganisms, and the ability to degrade and utilise cellulosic polysaccharides is limited to only a few bacterial and fungal groups. In nature, two different enzyme mechanisms for cellulose decomposition are utilised by bacteria and fungi; aerobic fungi and bacteria secrete high quantities of extracellular enzymes, whereas anaerobic bacteria and fungi possess cell-surface bound enzyme complexes (cellulosomes). Ruminant herbivores such as domestic cattle rely on symbiotic gut microorganisms for the digestion of plant material. Fibrobacter succinogenes is the type species of the genus Fibrobacter and was first isolated from the bovine rumen where it is established as the most prolific bacterial degrader of plant biomass. This superior efficiency to degrade cellulose in the rumen may be explained by recent evidence that within the genus Fibrobacter, a 'third' mechanism for the degradation of cellulose has evolved. F. succinogenes does not conform to the classical models of cellulose decomposition, and one possible mechanism for cellulose degradation in Fibrobacter involves the removal of individual cellulose fibres and subsequent transport through the outer membrane where they are cleaved by cellulases. Furthermore, molecular approaches have successfully identified members of the genus Fibrobacter in non-gut environments where cellulose is degraded (landfill sites and freshwater lakes), suggesting a greater diversity of fibrobacters than previously thought. Here, our approach is to sequence the genomes of several Fibrobacter strains that represent the breadth of ecological and taxonomic diversity currently detected within the genus. These analyses will include some novel strains of F. succinogenes that we have recently isolated from landfill sites and this is the first isolation of this species from a non-gut environment. Furthermore, these strains can utilise cellulose as the sole source of carbon for growth. Our comparative genomic analyses will enable us to investigate the evolutionary relatedness of the different strains and species within the Fibrobacter genus, with particular emphasis on the mechanism of cellulose degradation that we suspect is conserved across all members of the Fibrobacter genus and is the key physiological attribute that circumscribes the group. We will then focus on phenotypic characterisation of members of the genus, by observing the degradation and utilisation of polysaccharides and their derivatives by each strain, obtaining quantitative data on growth rates and enzyme activities. These data will provide important information on the hydrolytic abilities and substrate specificity of each strain, for which there is a currently a paucity of information. Finally, we will again use high throughput sequencing techniques, but this time focussing on gene expression profiles (mRNA) using transcriptomic approaches that inform on the differential expression of functional genes in response to growth on a range of polysaccharides and their derivatives. We will provide growth substrates that range from simple sugars to complex lignocellulosic plant biomass and compare gene expression profiles to enable us to implicate specific genes in particular degradative processes such as cellulose attachment or the transport of simple sugars. These data will provide a step change in our understanding of the mechanism for cellulose degradation employed by fibrobacters. It is clear that fibrobacters are prolific degraders of cellulose, and their enzymes may therefore find biotechnological application in improving the nutrition of economically important ruminant animals and in the refining of plant biomass for the production of bioethanol.

纤维素是地球上最丰富的有机多糖，是植物细胞壁的主要结构成分。因此，木质纤维素植物生物质在很大程度上难以被微生物分解，并且降解和利用纤维素多糖的能力仅限于少数细菌和真菌群。在自然界中，细菌和真菌利用两种不同的酶机制来分解纤维素；需氧真菌和细菌分泌大量胞外酶，而厌氧细菌和真菌则拥有细胞表面结合的酶复合物（纤维素体）。反刍草食动物（例如家牛）依靠共生肠道微生物来消化植物材料。产琥珀酸纤维杆菌是纤维杆菌属的模式种，首先从牛瘤胃中分离出来，在那里它被确定为最多产的植物生物质细菌降解剂。这种在瘤胃中降解纤维素的卓越效率可以通过最近的证据来解释，即在纤维杆菌属中，已经进化出一种纤维素降解的“第三种”机制。 F. succinogenes 不符合纤维素分解的经典模型，纤维杆菌中纤维素降解的一种可能机制涉及去除单个纤维素纤维并随后通过外膜运输，在外膜上它们被纤维素酶裂解。此外，分子方法已成功鉴定出纤维素降解的非肠道环境（垃圾填埋场和淡水湖）中的纤维杆菌属成员，这表明纤维杆菌的多样性比以前认为的要大。在这里，我们的方法是对几种纤维杆菌菌株的基因组进行测序，这些菌株代表了目前在该属内检测到的生态和分类多样性的广度。这些分析将包括我们最近从垃圾填埋场分离出的一些新的 F. succinogenes 菌株，这是该物种首次从非肠道环境中分离出来。此外，这些菌株可以利用纤维素作为生长的唯一碳源。我们的比较基因组分析将使我们能够研究纤维杆菌属内不同菌株和物种的进化相关性，特别强调纤维素降解机制，我们怀疑该机制在纤维杆菌属的所有成员中都是保守的，并且是关键的生理属性限制了该群体。然后，我们将通过观察每个菌株对多糖及其衍生物的降解和利用，获得生长速率和酶活性的定量数据，重点关注该属成员的表型特征。这些数据将提供有关每种菌株的水解能力和底物特异性的重要信息，而目前这方面的信息很少。最后，我们将再次使用高通量测序技术，但这次重点关注使用转录组学方法的基因表达谱 (mRNA)，该方法可了解功能基因响应于一系列多糖及其衍生物生长的差异表达。我们将提供从单糖到复杂木质纤维素植物生物质的生长底物，并比较基因表达谱，使我们能够在特定的降解过程（例如纤维素附着或单糖运输）中暗示特定基因。这些数据将使我们对纤维杆菌纤维素降解机制的理解发生重大变化。很明显，纤维杆菌是纤维素的多产降解者，因此它们的酶可以在生物技术中用于改善具有重要经济意义的反刍动物的营养以及精炼植物生物质以生产生物乙醇。

项目成果

Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs.

• DOI: 10.1016/j.syapm.2014.06.001
• 发表时间: 2014-10
• 期刊: Systematic and applied microbiology
• 影响因子: 3.4
• 作者: Emma Ransom-Jones;David L. Jones;A. Edwards;J. McDonald

Draft Genome Sequence of Clostridium sp. Strain W14A Isolated from a Cellulose-Degrading Biofilm in a Landfill Leachate Microcosm.

• DOI: 10.1128/genomea.00985-16
• 发表时间: 2016-09-22
• 期刊: Genome announcements
• 作者: Ransom-Jones E;McDonald JE
• 通讯作者: McDonald JE

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity.

• DOI: 10.1128/msphere.00300-17
• 发表时间: 2017-07
• 期刊: mSphere
• 影响因子: 4.8
• 作者: Ransom-Jones E;McCarthy AJ;Haldenby S;Doonan J;McDonald JE
• 通讯作者: McDonald JE