BUILDING OF PHYLOGENETIC TREES FOR MULTI-GENE FAMILY OF SM/LSM PROTEINS

SM/LSM 蛋白质多基因家族的系统发育树的构建

• 批准号: 7601365
• 负责人: PHILIP E BOURNE
• 金额: $ 0.03万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601365
• 关键词: Appearance; Archaea; Bacteria; Bacterial Genes; Code; Complex; Computer Retrieval of Information on Scientific Projects Database; Data Set; Disadvantaged; Eukaryota; Eukaryotic Cell; Event; Evolution; Excision; Facility Construction Funding Category; Family; Functional RNA; Funding; Gene Expression Regulation; Gene Family; Genes; Grant; Human; Institution; Introns; Methods; Open Reading Frames; Organism; Phylogenetic Analysis; Phylogeny; Process; Proteins; RNA; Research; Research Personnel; Resources; Running; Source; Speed; Spliceosomes; Stretching; Time; Trees; United States National Institutes of Health; interest; programs; reconstruction

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Reconstruction of early evolutionary events leading to appearance of spiceosomal introns in the last eukaryotic ancestor. Background: Spliceosomal complex is an intricate machinery which involves over 150 components of RNA and proteins; it is involved in the removal of non-coding stretches of sequences that often occur within coding regions of proteins. Emergence of the spliceosome in early eukaryotes is of intense interest the primary questions are how and when are still under intense debate. Since most of eukaryotic genes are interrupted by multiple introns (majority of the human genes has several introns each; these are frequently involved in the regulation of gene expression), the understanding the early evolution of introns and the machinery involved in their removal is of great importance. We are investigating a unique set of Sm and lsm proteins which are basal components of spliceosomal machinery. The proteins come from a multi-gene family in eukaryotes, but are singe copy genes within Archaea and Bacteria (these do not have spliceosomal machinery and thus this protein performs different function(s)). Among the questions we are investigating: (1) is it possible that archaeal and bacterial genes gave rise to eukaryotic multi-gene family; (2) can we connect archaeal and/or bacterial Sm/lsm gene to a specific eukaryotic gene(s); (3) what was the sequence of events during paralogous duplication of Sm genes in early eukaryotes; (4) how fast was the paralogous duplication? Many of these questions require construction of phylogenetic trees. Reasons for request: We are in the process of constructing phylogenetic trees for a large set of eukaryotic taxonomic families as well as representative of many of prokaryotic taxonomic . Such trees will give us information about ancestral relationships among eukaryotic genes and even more importantly as to where prokaryotic Sm/lsm proteins fit with respect to eukaryotic paralogous set. We are using a sensitive method for constructing phylogenetic trees, which is Bayesian inference method which is implemented in the MrBayes 3 phylogeny package (http://mrbayes.csit.fsu.edu/index.php). The drawback of this method is its notoriously long computational time. We are in disadvantage because we are dealing with many different organisms and a large multi-gene family; thus our dataset includes over 200 distinct sequences. Additionally due to relatively high level of similarity among sequences, we need to run the program for several million steps, which becomes an impossibly long task on a single machine. Right now each run involves 1-2 months on Dell Precision 670 machine. MrBayes has a parallel version of the code and which permits a significant speed-up and which hope to use, if granted TeraGrid allocation.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 真核生物最后一个祖先中spiceosomal内含子出现的早期进化事件的重建。背景资料：剪接体复合物是一种复杂的机制，涉及RNA和蛋白质的150多种组分;它参与去除经常出现在蛋白质编码区内的非编码序列。剪接体在早期真核生物中的出现引起了人们极大的兴趣，主要的问题是如何以及何时出现的，目前仍处于激烈的争论之中。由于大多数真核生物的基因都被多个内含子所打断（大多数人类基因都有几个内含子，这些内含子经常参与基因表达的调控），因此了解内含子的早期进化及其去除机制是非常重要的。我们正在研究一组独特的Sm和lsm蛋白质，这是剪接体机制的基础组成部分。这些蛋白质来自真核生物中的多基因家族，但在细菌和细菌中是单拷贝基因（这些没有剪接体机制，因此这种蛋白质执行不同的功能）。我们正在研究的问题包括：（1）古细菌和细菌基因是否可能形成真核生物多基因家族;（2）能否将古细菌和/或细菌Sm/lsm基因与一个特定的真核生物基因连接起来;（3）早期真核生物中Sm基因的旁系同源复制过程是怎样的;（4）旁系同源复制的速度有多快？这些问题中的许多需要构建系统发育树。申请理由：我们正在构建一个大的真核生物分类的家庭，以及许多原核生物分类的代表系统发育树的过程中。这样的树将给我们的真核基因之间的祖先关系的信息，甚至更重要的是，在原核Sm/lsm蛋白适合真核旁系同源集。我们正在使用一种敏感的方法来构建系统发育树，这是贝叶斯推理方法，它在MrBayes 3系统发育包（http：//mrbayes.csit.fsu.edu/index.php）中实现。这种方法的缺点是它的计算时间非常长。我们处于劣势，因为我们正在处理许多不同的生物和一个庞大的多基因家族;因此我们的数据集包括200多个不同的序列。此外，由于序列之间的相似性相对较高，我们需要运行程序数百万步，这在一台机器上是一项不可能完成的任务。目前，每次运行都需要在Dell Precision 670机器上运行1-2个月。MrBayes有一个并行版本的代码，它允许显着的速度提高，并希望使用，如果授予TeraGrid分配。