NSF/MCB-BSF: Rare genes and alleles in halophilic archaeal populations and communities

NSF/MCB-BSF：嗜盐古菌种群和群落中的稀有基因和等位基因

• 批准号: 1716046
• 负责人: Johann Peter Gogarten
• 金额: $ 81.73万
• 依托单位: University of Connecticut
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-07-15 至 2023-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1716046&HistoricalAwards=false
• 关键词: NSF; MCB; BSF; Rare; genes

The research will address the following questions: (1) How do microorganisms (bacteria and archaea) diverge and become adapted to new environments? (2) What is the role of rare genes in the adaptation process? Evolution and adaptation of bacterial and archaeal populations, the spread of "selfish" or parasitic genes in those populations, and especially the maintenance of within-lineage variation, in which different microbial cells contain slightly different complements of genes, impacts plant, animal and human life in many ways. This interdisciplinary project combines theoretical explorations with the study of environmental samples and laboratory experimentation on archaea that inhabit saline environments. The project will train its participants in theoretical and computational biology and genetic research that involves genome sequencing, genetic engineering and laboratory tests. The research will involve high-school students and teachers, undergraduate and graduate students, and postdoctoral fellows in an international collaboration to develop and test hypotheses on the long-term survival of rare genes. The research will execute the following tasks: (1) Through theory, modeling, and in silico experiments determine which population dynamics can lead to persistence of alleles in the non-core portion of the pan-genome. Find conditions that allow for the emergence of a within population division of labor, and for the within population survival of molecular parasites. In particular, explore the impact of population bottlenecks, gene flow and recombination within and between populations and species on the persistence of rare genes over time. (2) Determine which community dynamics can lead to the coexistence of alleles and to species diversification. Research will focus on the effect of low or uneven rates of within population gene transfer, possibly due to incompatibility of restriction modification (RM) or targeting by clustered regularly spaced short palindromic repeats (CRISPR) systems and we will explore when a division of labor that arose within a population is expected to lead to diversification. (3) Identify genes having limited distribution in Haloferax spp. and Halorubrum spp. populations and species from genome and meta-genome sequences, characterize these genes through bioinformatics based approaches, and select suitable candidates for genetic experimentation. (4) Perform experiments to determine the effect of selfish genetic elements, RM and CRISPR-Cas systems on recombination and gene frequencies in the off-spring. (5) Perform growth competition experiment in Hfx. volcanii (plus versus minus a gene of interest) to measure fitness cost of genes contributing to the production of a common shared good and for selfish genetic elements.This collaborative US/Israel project is supported by the Division of Molecular and Cellular Biosciences and the Office of International Science and Engineering at the US National Science Foundation and the Israeli Binational Science Foundation.

这项研究将解决以下问题：(1)微生物(细菌和古生菌)如何分化并适应新的环境？(2)稀有基因在适应过程中扮演什么角色？细菌和古生物种群的进化和适应，“自私”或寄生基因在这些种群中的传播，特别是维持谱系内变异，其中不同的微生物细胞含有略有不同的基因互补，以许多方式影响植物、动物和人类的生活。这个跨学科的项目结合了理论探索、环境样本研究和对生活在盐碱环境中的古生菌的实验室实验。该项目将对参与者进行理论和计算生物学以及涉及基因组测序、基因工程和实验室测试的遗传研究方面的培训。这项研究将让高中生和教师、本科生和研究生以及博士后研究员参与一项国际合作，以开发和测试关于稀有基因长期生存的假设。本研究将执行以下任务：(1)通过理论、建模和计算机实验确定哪些种群动态可以导致泛基因组非核心部分的等位基因持续存在。找到允许种群内出现分工和分子寄生虫在种群内生存的条件。特别是，探索种群瓶颈、种群和物种内部和物种之间的基因流动和重组对稀有基因随时间的持久性的影响。(2)确定哪些群落动态可以导致等位基因共存和物种多样性。研究将集中在低或不均匀的群体内基因转移率的影响，可能是由于限制性内切酶修饰(RM)的不相容或集群规则间隔短回文重复(CRISPR)系统的靶向，我们将探索群体内出现的分工何时有望导致多样化。(3)寻找在盐生植物中分布有限的基因。和Halorubrum spp.从基因组和元基因组序列中选择种群和物种，通过基于生物信息学的方法表征这些基因，并选择合适的候选基因进行基因实验。(4)进行自私遗传因素、Rm和CRISPR-Cas系统对子代重组和基因频率影响的实验研究。(5)在HFX上进行生长竞争实验。Volcanal II(加与减一个感兴趣的基因)，以衡量有助于生产共同利益和自私遗传元素的基因的适应成本。这一美国/以色列合作项目得到了美国国家科学基金会和以色列双国科学基金会分子和细胞生物科学部以及国际科学和工程办公室的支持。

项目成果

Identification and characterization of putative Aeromonas spp. T3SS effectors

• DOI: 10.1371/journal.pone.0214035
• 发表时间: 2019-06-04
• 期刊: PLOS ONE
• 影响因子: 3.7
• 作者: Rangel, Luiz Thiberio;Marden, Jeremiah;Gogarten, Johann Peter
• 通讯作者: Gogarten, Johann Peter

Halorubrum chaoviator Mancinelli et al. 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. Emended description of Halorubrum ezzemoulense Kharroub et al. 2006

• DOI: 10.1099/ijsem.0.003005
• 发表时间: 2018-11-01
• 期刊: INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
• 影响因子: 2.8
• 作者: Corral, Paulina;de la Haba, Rafael R.;Ventosa, Antonio
• 通讯作者: Ventosa, Antonio

Complete Genome Sequence of Halorubrum ezzemoulense Strain Fb21

• DOI: 10.1128/mra.00096-19
• 发表时间: 2019-03-01
• 期刊: MICROBIOLOGY RESOURCE ANNOUNCEMENTS
• 影响因子: 0.8
• 作者: Feng, Yutian;Louyakis, Artemis S.;Gogarten, J. Peter
• 通讯作者: Gogarten, J. Peter