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

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 重建导致在最后一个真核生物祖先中出现spiceosomal内含子的早期进化事件。背景：剪接体复合体是一种复杂的机制，涉及150多个RNA和蛋白质组分；它涉及去除经常出现在蛋白质编码区的非编码序列延伸。剪接体在早期真核生物中的出现引起了人们的浓厚兴趣，主要问题是剪接体是如何以及何时出现的，仍然存在激烈的争论。由于大多数真核基因都被多个内含子打断(大多数人类基因都有多个内含子，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具有重要意义。我们正在研究一组独特的Sm和LSM蛋白，它们是剪接体机械的基本成分。这些蛋白质来自真核生物中的多基因家族，但在古生物和细菌中是单拷贝基因(这些基因没有剪接体机制，因此这种蛋白质发挥不同的功能)(S)。我们正在研究的问题包括：(1)古生菌和细菌基因是否可能形成真核多基因家族；(2)我们能否将古生菌和/或细菌的Sm/Lsm基因与特定的真核基因(S)联系起来；(3)在早期真核生物中Sm基因的平行复制过程中发生了什么顺序；(4)平行复制的速度有多快？其中许多问题需要构建系统发育树。查询理由：我们正在构建一大套真核生物分类家族的系统发育树，同时也是许多原核分类的代表。这样的树将为我们提供关于真核基因之间的祖先关系的信息，更重要的是，关于原核生物Sm/Lsm蛋白相对于真核类同源集合的位置。我们正在使用一种敏感的方法来构建系统发生树，这就是在MR Bayes3系统发展包(http://mrbayes.csit.fsu.edu/index.php).)中实现的贝叶斯推理方法这种方法的缺点是其计算时间长得出名。我们处于劣势，因为我们正在处理许多不同的生物体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水平相对较高，我们需要运行该程序数百万步，这在一台机器上成为一项不可能的长任务。目前，每次运行都需要在Dell Precision 670计算机上运行1-2个月。Bayes先生有一个并行版本的代码，它允许显著的加速，并希望使用，如果获得TeraGrid分配的话。

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.