Physiological Advantages of the Development of Bacterial Morphology

细菌的形状和大小的星座既神秘又引人注目。 为什么有些细菌种类会呈现出弹簧圈、星星或吃了一半的甜甜圈等不同的形状？ 没人知道 然而，这些形状的精确繁殖和进化保守表明它们在细菌的生活中发挥着重要作用。 尽管最近在理解控制细胞形状决定或形态发生的机制方面取得了进展，但我们仍然不了解细菌细胞如何产生特定的形状，或者细菌形态变化的功能是什么。 该项目将重点关注一组细菌，即prosthecate或stalked细菌，它提供了一个明确的和简单的形态变化的例子，其研究将揭示适用于其他细胞形状变化的基本原理。 有柄细菌合成了一个或多个细胞包膜的薄延伸部分，即前囊或柄，它们充当某种天线，增强了它们从环境中吸收营养的能力。 狭窄的茎几乎没有增加细胞的体积，进入的营养物质向细胞的主体扩散，在那里营养物质通过代谢过程迅速吸收。 该项目的目标是产生一个高质量的草案序列的九个基因组的prosthecate细菌，和一个密切相关的非prosthecate细菌，选择代表越来越复杂的形态集合。 基因组将进行分析，相对于秸秆的生物合成和功能的机制，秸秆生物合成的调节途径的保护程度，以及这些生物体的有趣和潜在有用的生理特性。 通过对这些细菌基因组序列的比较分析，将有助于进一步了解菌柄的合成机制。 这些结果将为工程化具有新代谢途径的茎细菌或工程化其他细菌合成茎提供必要的信息。本研究中获得的基因组序列信息将有助于许多研究细胞生物学、发育生物学以及细菌的细胞形状确定和功能的研究人员的研究。 有柄细菌是水生环境中普遍存在的居民，在低营养（寡营养）条件下茁壮成长。 因此，这项研究将提供深入了解一般的寡养生物的生理。 由于秸秆从水源中吸收扩散化合物，因此可以利用这一特征进行生物修复，特别是从受污染的水源中吸收有毒化合物。 通过改造用于生物修复的细菌使其成为秸秆，可以提高它们吸收污染物的能力和效率。 待测序的有柄细菌在生理上是多样的，包括缺氧细菌和需氧细菌。 我们应该可以设计出特定种类的有柄细菌来对抗特定环境中的污染，无论是利用它们的代谢途径，还是用其他生物的代谢途径来改造它们。 此外，来自某些有柄细菌的胞外多糖可螯合金属，这一特征可用于修复受金属毒性影响的环境。 在这个项目中获得的知识也可以在工业中使用。 细菌经常被用作将一种分子大量转化为另一种分子的工具。 例如，通过改造这些细菌来合成秸秆，提高这些细菌吸收底物分子的速度，应该可以提高药物生产。 具有生态学意义的是，具有秸秆的细菌普遍存在于地球上所有的水生环境中，并且秸秆已被证明可以提高磷的吸收。 磷是决定湖泊和海洋生产力的限制性营养素。 这些被跟踪的细菌是清除海洋和湖泊中的磷并将其重新引入食物链的核心角色。 最后，该项目还将提供基因组学方面的培训机会。 参与PI实验室的这个项目和其他项目的学生和博士后研究员将有机会在PI的监督下指导经验不足的学生。 参与PI研究的学生，包括本科生，将接触到基因组分析的现代方法及其在工业和生物修复中应用的工程细菌。 最后，基于本研究的查询模块将开发用于本科微生物学实验室课程。

The constellation of shapes and sizes among bacteria is as remarkable as it is mysterious. Why should some bacterial species adopt such diverse shapes as a bedspring coil, a star or a partly eaten donut? No one really knows. However, the precise reproduction and evolutionary conservation of these shapes indicate that they play an important role in the life of bacteria. Despite recent progress in understanding the mechanisms that control cell shape determination, or morphogenesis, we still do not understand how bacterial cells generate specific shapes, or what the function of bacterial morphological changes is. This project will focus on a group of bacteria, the prosthecate or stalked bacteria, that provides a well-defined and simple example of morphological change, whose study will reveal basic principles that apply to other cell shape changes. Stalked bacteria synthesize one or more thin extensions of their cell envelope, the prosthecae or stalk, that act as sort of antennae that amplify their ability to take up nutrients from their environment. The narrow stalk adds little volume to the cell, and incoming nutrients diffuse toward the cell's main body, where nutrients are quickly assimilated by metabolic processes. The goal of this project is to produce a high quality draft sequence of nine genomes of prosthecate bacteria, and one closely related non-prosthecate bacterium, selected to represent an increasingly complex collection of morphologies. The genomes will be analyzed with respect to mechanisms for the biosynthesis and function of stalks, the extent of conservation of regulatory pathways for stalk biosynthesis, and the interesting and potentially useful physiological properties of these organisms. Comparative analysis of the genome sequences of the stalked bacteria will further the understanding of the mechanisms of stalk synthesis. The results will provide the information necessary to engineer stalked bacteria with new metabolic pathways, or to engineer other bacteria to synthesize stalks. The genomic sequence information obtained in this study will aid the research of many investigators who study the cell biology, developmental biology, and cell shape determination and function of bacteria. Stalked bacteria are ubiquitous inhabitants of aquatic environments and thrive under low nutrient (oligotrophic) conditions. Therefore, this study will provide insight into the physiology of oligotrophs in general. Since stalks take up diffuse compounds from water sources, this feature could be exploited for bioremediation, specifically the uptake of toxic compounds from contaminated water sources. By engineering the bacteria used in bioremediation to make stalks, their ability to take up pollutants and their efficiency can be improved. The stalked bacteria to be sequenced are physiologically diverse, including both anoxygenic and aerobic bacteria. It should be possible to design specific genera of stalked bacteria to combat contamination in specific environments, either by exploiting their metabolic pathways, or by engineering them with metabolic pathways from other organisms. Furthermore, extracellular polysaccharides from some of the stalked bacteria sequester metals, a feature that could be used to remediate environments affected by metal toxicity. The knowledge acquired in this project could also have uses in industry. Bacteria are often used as workhorses in the mass-conversion of one molecule to another. For example, improving the speed of uptake of a substrate molecule by these bacteria, by engineering them to synthesize stalks, should improve drug production. Of ecological significance, bacteria with stalks are ubiquitous in all the earth's aquatic environments, and stalks have been shown to improve the uptake of phosphorus. Phosphorus is a limiting nutrient in determining the productivity of lakes and oceans. The stalked bacteria are central players in scavenging phosphorus in oceans and lakes, and reintroducing it into the food chain. Finally, this project will also provide training opportunities in genomics. Students and postdoctoral fellows involved in this and other projects in the PI's laboratory will have the opportunity to mentor less experienced students under the supervision of the PI. Students involved in the PI's research, including undergraduate students, will be exposed to modern methods of genomic analysis and their use to engineer bacteria for applications in industry and bioremediation. Finally, inquiry-based modules based on this research will be developed for use in undergraduate microbiology laboratory courses.