New approaches to resolving community metaproteomes: ComProt

解析群落宏蛋白质组的新方法：ComProt

• 批准号: NE/S013539/1
• 负责人: Elizabeth Wellington
• 金额: $ 6.42万
• 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: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FS013539%2F1
• 关键词: New; approaches; resolving; community; metaproteomes

Understanding interactions between organisms in an ecosystem is a critical part of ecological research and facilitates our understanding of how ecosystems function and this is particularly important for microorganisms and microarthropods as they are often difficult to study in situ in real time. Currently the natural environment faces many challenges and we need to be able to measure the impacts of changes in climate, pollutant levels, intensive farming and development of ley systems to understand how resilient communities are and how Carbon, nitrogen and phosphorous cycles are affected.Microrganisms play a vital role in our environment they occupy a wide range of habitats from our gut and body surfaces all the way to hot vents under the sea, they are critical in the soil for recycling of nutrients and plant health and responsible for the essential digestion of cellulose from grass being broken down in the specialised stomach of the cow termed the rumen to the global cycling of carbon in the oceans via harvesting of sunlight as many bacteria can photosynthesize and thus harvest light energy to fix carbon dioxide. A major problem exists in our ability to study the physiology and overall activities of these microbes due to the fact that we cannot isolate and cultivate (yet) the vast majority (probably over 98%) of them in the laboratory. We know they exist because we have used methods similar to DNA forensic approaches to detect them solely based on their DNA using signature genes which allow us to identify and group them. Most of this diversity is bacterial but there are also several groups of fungi. New methods are being developed for the study of these microbial populations and this is called metagenomics and we are focused in this projects on the proteins produced termed metaproteomic. Proteins equate with activity as all enzymes are proteins and act as catalysts for reactions. Therefore, we can use the metagenomes to help in identifying which proteins are present because there is a relationship between the DAN code and the sequence of peptides in a protein. Making this link is challenging so we aim to improve the understanding of how to translate a series of peptide sequences into functioning proteins and recognise both their origins and putative function.so that we study the microbial community as a population of many genomes rather than trying to isolate and study one. We can study this population in our guts or in the soil by extracting and analysing DNA for diversity analysis, RNA for gene expression and protein for confirmation of activities and metabolites to determine physiology. In addition we can extract DNA and express it in other bacteria which are culturable. This allows us to capture the DNA and express it thus gaining an insight into some functions such as specific enzymes or pigments with special properties. The imof the proposed work is to establish a network of academic partners to build capacity in this important area of science to ensure that we are able to study and exploit all the interesting and exciting attributes of bacterial populations and harness them for a sustainable future.

了解生态系统中生物之间的相互作用是生态研究的关键部分，有助于我们了解生态系统的功能，这对微生物和微节肢动物尤其重要，因为它们通常很难在现场实时研究。目前，自然环境面临着许多挑战，我们需要能够衡量气候变化、污染物水平、集约化农业和生态系统发展的影响，以了解社区的恢复能力以及碳、氮和磷循环是如何受到影响的。微生物在我们的环境中起着至关重要的作用，它们占据了广泛的栖息地，从我们的肠道和身体表面一直到海底的热喷口，它们在土壤中对养分的循环和植物健康至关重要，并负责消化牛的特殊胃（称为瘤胃）中分解的草中的纤维素，以及通过收集阳光在海洋中进行碳的全球循环，因为许多细菌可以进行光合作用，从而收集光能来固定二氧化碳。我们研究这些微生物的生理和整体活动的能力存在一个主要问题，因为我们（目前）还不能在实验室中分离和培养绝大多数（可能超过98%）微生物。我们知道它们的存在，因为我们使用了类似于DNA法医方法的方法来检测它们，仅仅基于它们的DNA，使用特征基因，使我们能够识别和分类它们。这种多样性主要是细菌，但也有几类真菌。研究这些微生物种群的新方法被称为宏基因组学，我们在这个项目中关注的是被称为宏基因组学的蛋白质。蛋白质等同于活性，因为所有的酶都是蛋白质，并作为反应的催化剂。因此，我们可以使用宏基因组来帮助识别哪些蛋白质存在，因为DAN代码与蛋白质中的肽序列之间存在关系。建立这种联系是具有挑战性的，因此我们的目标是提高对如何将一系列肽序列翻译成功能蛋白质的理解，并识别它们的起源和假定的功能。因此，我们将微生物群落作为许多基因组的群体来研究，而不是试图分离和研究一个基因组。我们可以通过提取和分析DNA来进行多样性分析，提取和分析RNA来进行基因表达，提取和分析蛋白质来确定活性和代谢产物，从而确定生理学。此外，我们可以提取DNA并将其表达在其他可培养的细菌中。这使我们能够捕获DNA并表达它，从而深入了解某些功能，例如具有特殊性质的特定酶或色素。拟议工作的目的是建立一个学术合作伙伴网络，以建立这一重要科学领域的能力，以确保我们能够研究和利用细菌种群的所有有趣和令人兴奋的属性，并利用它们实现可持续的未来。

项目成果

Transporter characterisation reveals aminoethylphosphonate mineralisation as a key step in the marine phosphorus redox cycle.

• DOI: 10.1038/s41467-021-24646-z
• 发表时间: 2021-07-27
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Murphy ARJ;Scanlan DJ;Chen Y;Adams NBP;Cadman WA;Bottrill A;Bending G;Hammond JP;Hitchcock A;Wellington EMH;Lidbury IDEA
• 通讯作者: Lidbury IDEA

Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions.

• DOI: 10.1128/msystems.00025-22
• 发表时间: 2022-08-30
• 期刊: mSystems
• 影响因子: 6.4