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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

基本信息

批准号：
8488446
负责人：
Betsy Anne Read
金额：
$ 10.6万
依托单位：
CALIFORNIA STATE UNIVERSITY SAN MARCOS
依托单位国家：
美国
项目类别：
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/8488446
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

项目摘要

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.

描述（由申请人提供）：颗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300多种，每种都有独特的碳酸钙细胞覆盖。虽然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有关的信息。大分子，特别是蛋白质，协调晶体生长过程和决定球石纳米级结构的方式尚不清楚。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和海洋颗石藻特有的方解石板的纳米级形状和图案。这项研究的主要假设是，控制球石合成的设计原则只能通过识别和表征参与其合成和组装的基因和基因产物来确定。Emiliania huxleyi（E. huxleyi）被认为是模式颗石藻，因为它的数量多，分布广，而且容易培养。它的基因组最近在我们的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。我们建议在此解剖生物矿化和调节机制，需要协调这一复杂的过程，通过应用比较转录组学的方法。为此，我们建议1）使用高通量454测序来询问已知影响生物矿化的营养条件下的三个姐妹物种（两个钙化和一个非钙化）的转录组，以及2）通过检查被认为对钙化过程至关重要的功能相关基因组的启动子序列来鉴定顺式调节元件。这项工作将提供一个强大的和完整的生物矿化转录组和潜在的顺式作用调控元件的视图。作为一个合作的努力，依赖于微生物学，基因组学和分子细胞生物学，生物信息学和计算生物学的专业知识，这一建议有望为科学家提供一个宝贵的资源，努力了解在这个重要的模型系统中的生物矿化的调节和控制。