Collaborative Research: Iron limitation, carbon metabolism and siderophore production in marine bacteria - a systems biology approach

合作研究：海洋细菌中的铁限制、碳代谢和铁载体产生——一种系统生物学方法

• 批准号: 0929203
• 负责人: Elizabeth Mann
• 金额: $ 40.48万
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0929203&HistoricalAwards=false
• 关键词: Collaborative; Research; Iron; limitation; carbon

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).Iron limitation of heterotrophic bacteria has substantial biogeochemical implications, including lower assimilation efficiencies and reduced incorporation of CO2 into biomass. Marine bacterioplankton also have a large impact on iron speciation in seawater through their production of siderophores, ligands with a high affinity for iron. Over 99.9% of the dissolved iron in seawater is strongly bound to organic ligands, which are likely to include siderophores since they have functional groups and conditional stability constants for iron that are similar to chelators detected in situ. Iron limitation and siderophore synthesis are linked since these ligands are produced specifically in response to low intracellular iron concentrations. Neither process is completely understood in marine bacteria. For instance, the production of iron binding ligands in seawater unexpectedly increases, not decreases when iron is added to HNLC regions. One possible explanation is the role of carbon, which complicates studies of both iron limitation and siderophore synthesis. The extent to which low iron concentrations reduce bacterioplankton growth efficiencies or productivity in situ is not well-quantified because of the rapid stimulation of primary production that occurs after iron limitation of phytoplankton is relieved. The resulting increase in available carbon makes it is difficult to distinguish between direct and indirect iron (i.e. carbon) limitation of marine bacteria. Carbon source and availability may also play a secondary but important role in regulating siderophore production, which can be either stimulated or repressed by the addition of glucose. The objective of this project is to model the interacting gene regulatory networks that control iron acquisition and carbon metabolism in gamma -proteobacteria, specifically Vibrio fischeri. Iron and carbon regulatory pathways are tightly linked in a complex web of relationships mediated by global transcriptional regulators (Fur and CRP) and the small RNA RyhB. In order to construct a gene regulatory network model, the PIs will use an integrated systems biology approach that combines computational, bioinformatics based research and laboratory experimentation. Predictions of gene expression, siderophore production and the flux of iron with changing environmental conditions will be validated by quantifying gene expression using qRT-PCR and global transcriptome analyses, as well as determining iron quotas and iron uptake rates. Intellectual Merit: This study will contribute to the general understanding of iron speciation in the upper ocean by elucidating the interactions between iron and carbon limitation, carbon source and siderophore production. The gene regulatory network model will be capable of identifying environmental variables critical to siderophore production and evaluating potential biomarkers for iron limitation. This project will facilitate the discovery of new genes and control mechanisms involved in iron metabolism and shed light on other processes such as virulence and luminescence, which utilize the same or similar interactions and transcription factors. Finally, this approach also provides a framework for synthesizing information on the genetic level and using it to make predictions about processes such as siderophore production that are ecologically important. Broader Impacts: This project will enhance infrastructure for scientific research and education by mentoring young scientists and supporting both outreach programs and course development at several educational levels. Support is requested for graduate students to participate in the proposed research and all three PIs will recruit undergraduates for summer internships, often targeting underrepresented groups. Research Experiences for Teachers supplements are requested to allow two high school science educators to participate in our research at the Skidaway Institute of Oceanography and design a laboratory exercise that will illustrate how microbes respond to nutrient limitation. The aim is to provide a research experience that will strengthen collaborations among educators at both the local and national levels.

该奖项是根据2009年的《美国复苏与再投资法》（公共法第111-5）资助的。异营养细菌的铁限制具有实质性的生物地球化学意义，包括较低的同化效率和将CO2纳入生物量。海洋细菌脑浮游生物还通过产生铁载体，对铁的高亲和力的配体，对海水的铁物种形成产生了很大影响。海水中溶解的铁的99.9％与有机配体密切结合，有机配体可能包括铁载体，因为它们具有功能组和铁的条件稳定性常数类似于原位检测到的螯合剂。铁的限制和铁载体合成是连接的，因为这些配体是针对低细胞内铁浓度而专门产生的。在海洋细菌中，这两种过程均被完全理解。例如，海水中铁结合配体的产生意外增加，当将铁添加到HNLC区域时不会减少。一种可能的解释是碳的作用，它使对铁的限制和铁载体合成复杂化。低铁浓度降低细菌的生长效率或原位生产力的程度并没有得到充分的质量，因为在铁限制浮游植物之后，迅速刺激了原发性产生。所产生的可用碳的增加使得很难区分海洋细菌的直接和间接铁（即碳）限制。碳源和可用性也可能在调节铁载体产生中起次要但重要的作用，这可以通过添加葡萄糖来刺激或抑制。 该项目的目的是建模相互作用的基因调节网络，该网络控制伽马 - 细菌，特别是弧菌fischeri中的铁采集和碳代谢。铁和碳调节途径在由全球转录调节器（Fur和CRP）和小RNA RYHB介导的复杂关系中紧密相关。为了构建基因调节网络模型，PI将使用一种集成的系统生物学方法，该方法结合了基于计算，基于生物信息学的研究和实验室实验。通过使用QRT-PCR和全局转录组分析来量化基因表达，并确定铁配额和铁的吸收率，可以通过量化基因表达来验证基因表达，铁载体产生和铁的通量的预测。 知识分子的优点：这项研究将通过阐明铁与碳限制，碳源和铁载体生产之间的相互作用，从而有助于对上海中的铁物种形成的普遍理解。基因调节网络模型将能够识别对铁载体产生至关重要的环境变量，并评估潜在的生物标志物以实现铁的限制。该项目将促进与铁代谢有关的新基因和控制机制的发现，并阐明其他过程，例如毒力和发光，这些过程利用了相同或相似的相互作用和转录因子。最后，这种方法还提供了一个框架，以合成有关遗传水平的信息，并使用它来对诸如生态重要的铁载体产生等过程进行预测。 更广泛的影响：该项目将通过指导年轻科学家并支持多个教育水平的外展计划和课程发展来增强科学研究和教育的基础设施。要求研究生参加拟议的研究，所有三个PI都将招募暑期实习生，通常针对代表人数不足的群体。要求教师补充剂的研究经验，以允许两名高中科学教育者参加Skidaway海洋学和设计研究所的研究，这将说明微生物对营养限制的反应。目的是提供研究经验，以加强地方和国家一级的教育者之间的合作。