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，代表了植物细胞壁的主要结构成分。因此，木质纤维素植物的生物量在很大程度上是微生物分解的顽固性，并且降解和利用纤维素多糖的能力仅限于几个细菌和真菌群。在本质上，细菌和真菌利用了两种用于纤维素分解的酶机制。有氧真菌和细菌分泌大量的细胞外酶，而厌氧菌和真菌具有细胞表面结合的酶复合物（纤维素体）。家庭牛等反刍动物的食草动物依靠共生肠道微生物来消化植物材料。纤维杆菌琥珀酸酯是纤维杆菌属的类型，首先是从牛瘤胃中分离出来的，在牛瘤胃中，它被确定为植物生物量最多产的细菌降解者。最近的证据表明，在瘤胃中降解纤维素的较高效率可以解释，即在纤维细菌属中，纤维素降解的“第三个”机制已经发展。 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，然后通过外膜通过纤维素酶裂解的外膜进行运输。此外，分子方法已成功地鉴定出纤维素降解（垃圾填埋场和淡水湖泊）的非粉状环境中的纤维杆菌属成员，这表明纤维杆菌的多样性比以前想到的更大。在这里，我们的方法是对几种代表当前在该属中检测到的生态和分类多样性广度的几种纤维杆菌菌株的基因组进行测序。这些分析将包括一些我们最近从垃圾填埋场分离出来的新型F. succinogenes菌株，这是该物种从非旋转环境中的第一个隔离。此外，这些菌株可以利用纤维素作为生长的唯一碳来源。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，并特别强调了纤维素降解的机制，我们怀疑，在纤维杆菌属的所有成员中，我们都保留了纤维杆菌的所有成员，并且是概括组的关键生理属性。然后，我们将通过观察每种菌株的降解和利用来降解和利用多糖及其衍生物，以获取有关生长速率和酶活性的定量数据，从而关注该属成员的表型表征。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，目前的信息很少。最后，我们将再次使用高吞吐量测序技术，但是这次使用转录组方法着眼于基因表达谱（mRNA），这些方法将功能基因的差异表达告知，以响应一系列多糖及其衍生物的生长。我们将提供从简单糖到复杂的木质纤维素植物生物量的生长底物，并比较基因表达谱，使我们能够将特定基因牵连到特定的降解过程，例如纤维素附着或简单糖的运输。这些数据将在我们对纤维杆菌采用的纤维素降解机制的理解中提供一个步骤变化。显然，纤维杆菌是纤维素的多产降解剂，因此它们的酶在改善经济上重要的反刍动物的营养以及植物生物量以生产生物乙醇时可以发现生物技术的应用。

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