Dissecting Biomineralization by Mining the Transcriptome of Three Closely Related

通过挖掘三个密切相关的转录组来剖析生物矿化

• 批准号: 8278504
• 负责人: Betsy Anne Read
• 金额: $ 10.99万
• 依托单位: CALIFORNIA STATE UNIVERSITY SAN MARCOS
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2014-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8278504
• 关键词: Address; Affect; Architecture; Attention; Automobile Driving; Bicarbonates; Binding Sites; Bioinformatics; Biological; Biological Models; Biology; Calcified; Calcite; Calcium; Calcium Carbonate; Cells; Cellular biology; Characteristics; Collaborations; Complex; Computational Biology; Data; Department of Energy; Development; Engineering; Gene Expression; Gene Expression Profile; Genes; Genetic Transcription; Genome; Genomics; Geology; Goals; Growth; Health Technology; Healthcare; High temperature of physical object; Human; Journals; Kidney Calculi; Knowledge; Laboratories; Lead; Life; Manuscripts; Marines; Medicine; Membrane; Microbiology; Mining; Modeling; Molecular; Molecular Profiling; Northern Blotting; Nutrient; Osteoporosis; Pattern; Physiological; Phytoplankton; Process; Production; Proteins; Publishing; Regulation; Regulator Genes; Regulatory Element; Research; Resources; Reverse Transcriptase Polymerase Chain Reaction; Rickets; Science; Scientist; Sequence Analysis; Shapes; Signal Transduction; Sister; Skeleton; Structure; Technology; Time; Tissues; Tooth structure; Transcript; Variant; Vascular calcification; Work; Writing; biomineralization; bone; calcification; calcium bicarbonate; comparative; design; genetic regulatory protein; implantable device; improved; insight; life history; macromolecule; member; mineralization; nanoscale; novel; programs; promoter; public health relevance; research study; response; scaffold; trait; transcription factor; transcriptomics

DESCRIPTION (provided by applicant): Coccolithophores are one of the most spectacular calcifying microalgae. They are the third most prominent group of phytoplankton with over 300 extant species, each of which displays a unique calcium carbonate cell covering. While the calcareous skeletons otherwise known as coccoliths, have attracted the attention of scientists from diverse fields, information relating to the function and molecular complexity of the underlying biomineralization processes is lacking. The manner in which macromolecules, in particular proteins, orchestrate the crystal growth processes and dictate the nanoscale architecture of the coccoliths is not known. Hence, the broad and long term objective of our laboratory is to understand the molecular underpinnings of biomineralization and the nanoscale shape and patterning of the calcite plates characteristic of marine coccolithophores. The major hypothesis underlying this research is that the design principles governing the synthesis of coccoliths can only be determined by identifying and characterizing the genes and gene products involved in their synthesis and assembly. Emiliania huxleyi (E. huxleyi) is recognized as the model coccolithophore because of its abundance, cosmopolitan distribution, and the ease with which it can be cultured. Its genome was recently sequenced in a collaborative effort between our laboratory and the U.S. Department of Energy, making it feasible to apply various global approaches to explore biomineralization. We propose herein to dissect biomineralization and the regulatory mechanisms required to coordinate this complex process by applying a comparative transcriptomics approach. To this end, we proposed to 1) use high throughput 454 sequencing to interrogate the transcriptome of three sister species (two calcifying and one non-calcifying) under nutrient conditions known to affect biomineralization, and 2) to identify cis-regulatory elements by examining the promoter sequences of functionally related sets of genes deemed critical to the calcification processes. This work will afford a robust and complete view of the biomineralization transcriptome and potential cis-acting regulatory elements. As a collaborative effort that relies on expertise in microbiology, genomics and molecular cell biology, bioinformatics and computational biology, this proposal promises to provide a valuable resource for scientists working to understand the regulation and control of biomineralization in this important model system. PUBLIC HEALTH RELEVANCE: Scientists and engineers are eager to understand the biological controls that govern calcification for applications related to human health and technology. Insight into the molecular mechanisms regulating these processes in E. huxleyi may lead to new strategies to promote healthy mineralization and address problems associated with pathological conditions such as rickets, kidney stones, osteoporosis, and ectopic calcification of vascular tissues.

描述（申请人提供）：球石藻是最壮观的钙化微藻之一。它们是第三大浮游植物群，现存物种超过300种，每一种都有独特的碳酸钙细胞覆盖。虽然这些钙质骨骼也被称为球石，吸引了来自不同领域的科学家的注意，但缺乏与潜在生物矿化过程的功能和分子复杂性相关的信息。大分子（尤其是蛋白质）如何协调晶体生长过程，并决定了球石的纳米级结构，目前尚不清楚。因此，我们实验室的广泛和长期目标是了解生物矿化的分子基础，以及海洋颗石群特征的方解石板的纳米级形状和图案。本研究的主要假设是，控制球粒合成的设计原则只能通过鉴定和表征参与其合成和组装的基因和基因产物来确定。埃米利亚·赫胥黎（E. huxleyi）被认为是典型的颗石藻，因为它的丰富，世界性分布，和容易培养。它的基因组最近在我们实验室和美国能源部的合作下进行了测序，使得应用各种全球方法来探索生物矿化成为可能。在此，我们建议通过应用比较转录组学方法来剖析生物矿化和协调这一复杂过程所需的调节机制。为此，我们提出1)在已知影响生物矿化的营养条件下，使用高通量454测序来询问三个姊妹物种（两个钙化和一个非钙化）的转录组；2)通过检查对钙化过程至关重要的功能相关基因集的启动子序列来鉴定顺式调控元件。这项工作将为生物矿化转录组和潜在的顺式调控元件提供一个强大而完整的观点。作为一项依靠微生物学、基因组学和分子细胞生物学、生物信息学和计算生物学专业知识的合作努力，该提案有望为科学家们了解这一重要模型系统中生物矿化的调节和控制提供宝贵的资源。