Molecular Evolution and Adaptation of Microbial Polyketide Biosynthetic Sequences

微生物聚酮化合物生物合成序列的分子进化和适应

• 批准号: 9974984
• 负责人: Jose Lopez
• 金额: $ 24.99万
• 依托单位: Harbor Branch Oceanographic Institution, Inc.
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-09-01 至 2004-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9974984&HistoricalAwards=false
• 关键词: Molecular; Evolution; Adaptation; Microbial; Polyketide

LopezPolyketide (PK) compounds and their biosynthetic enzymes represent diverse phenotypes in microorganisms, but the underlying causes for this diversity are not completely understood. The major hypothesis of this research is that biosynthetic polyketide synthase (PKS) sequence diversity and "programming" is driven by positive diversifying selection and accounts for the majority of polyketide metabolite diversity observed in nature. A comparative bioinformatics approach will be implemented to achieve the following objectives: a) Infer the secondary and higher order enzyme structures of published PKS loci, such as those coding for erythromycin, rapamicin, and rifamycin by comparisons with fatty acid synthases (FAS) or by using bioinformatics software such as FIREBIRD; b) Compare sequences and predicted enzyme structures of "paralogous" modules (within a single PK pathway) and correlate these with corresponding PK metabolite or PK intermediates and infer possibility of gene duplications; c) Compare orthologous (between different bacteria and different pathways) PKS enzyme module sequences and structures to obtain correlations with PK metabolite end products and also to investigate the possibility and frequency of horizontal gene transfer; d) If PKS structures appear structurally homologous, determine specific residues and codons in primary sequences which are pivotal for structural determination, while if structures are not homologous, investigate how active centers remain functional, and why they are conserved, using data on predicted structural conformations; e) Determine whether codons and residues which appear pivotal for structure determination and overall enzyme function are positively selected (to preserve analogous/homologous structures or function); f) Isolate several new or longer PKS gene sequence segments from marine microbes previously characterized from the HBOI collection. Through these analyses, a model of molecular adaptation based on the evolution of PKS enzyme sequence, structure, and function will be formulated and integrated with the biosynthesis of the ultimate phenotypic products (PK metabolites). Public ImpactNature manifests its diversity at numerous levels, with one being the biochemical diversity of natural products. Understanding the fundamental bases of this diversity, at cellular, genetic and molecular levels, will facilitate the harnessing of natural products, such as polyketide antibiotics, for practical purposes. However a large knowledge gap exists between genetic sequence data and their phenotypes, the physical expression of genes, which this research aims to fill. Still, molecular sequence information can be used for tracking the evolutionary history, inferring molecular structures and obtaining the contemporary ecological context of certain genes coding for polyketide natural products. Moreover, despite the many natural compounds with therapeutic potential that have been discovered, the supply of those products is often less than optimal. This research can have a direct impact on polyketide supply issues since the target of study are the genes involved in the biosynthesis of polyketide compounds.

Lopezpolyketide（PK）化合物及其生物合成酶代表微生物中的各种表型，但是这种多样性的潜在原因尚未完全理解。这项研究的主要假设是，生物合成聚酮化合酶（PKS）序列多样性和“编程”是由积极多样化的选择驱动的，并且是大多数在自然界观察到的聚酮化代谢物多样性。 将实施一种比较生物信息学方法来实现以下目标：a）通过与脂肪酸合成酶（FAS）或使用BioInformatics的Firfirfirdsick进行比较，推断出已发表的PKS基因座的二级和高阶酶结构，例如为红霉素，雷帕美霉素和利由木素编码的酶结构。 b）比较“寄生态”模块（在单个PK途径中）的序列和预测酶结构，并将其与相应的PK代谢物或PK中间体相关联，并推断基因重复的可能性； c）比较直系同源（在不同的细菌和不同途径之间）PKS酶模块序列和结构以获得与PK代谢产物的相关性，并研究水平基因转移的可能性和频率； d）如果PKS结构在结构上同源，请在主要序列中确定特定的残基和密码子，这些残基和密码子是结构确定的关键，而如果结构不是同源的，请研究活动中心如何保持功能以及为什么使用预测结构结构的数据； e）确定是否积极地选择了对于结构确定和总体酶功能关键的密码子和残基（以保留类似/同源结构或功能）； f）与先前从HBOI收集中表征的海洋微生物分离出几个新的或更长的PKS基因序列段。 通过这些分析，将基于PKS酶序列，结构和功能的演化的分子适应模型，并将其与最终表型产物（PK代谢物）的生物合成配合并整合。公共影响力在许多层面上都表现出其多样性，其中一种是天然产品的生化多样性。 了解这种多样性的基本基础，在细胞，遗传和分子水平上，将促进用于实际目的的天然产物（例如聚酮化合物抗生素）的利用。然而，遗传序列数据及其表型之间存在很大的知识差距，即基因的物理表达，这项研究旨在填补这一基因。 尽管如此，分子序列信息仍可用于跟踪进化史，推断分子结构并获得编码聚酮化合物天然产物的某些基因的当代生态环境。此外，尽管已经发现了许多具有治疗潜力的天然化合物，但这些产品的供应通常不足以最佳。 这项研究可能会对聚酮化合物供应问题产生直接影响，因为研究的目标是与聚酮化合物的生物合成有关的基因。