Using Co-culture and Bioinformatics to Discover New Antibiotic Bioactivities

 描述(由申请人提供) 对常用抗生素产生抗药性的致病细菌的发病率出现了惊人的上升。因此，我们迫切需要确定更多用作抗生素的分子。细菌本身历来是抗生素和其他相关“次生代谢物”的最佳来源。虽然最常见和最丰富的微生物抗生素已经作为“容易摘到的水果”收获，但微生物仍然是新的次生代谢物的深层次潜在来源。然而，获得这些化合物的一个关键障碍是，细菌在实验室培养时很少产生完整的次生代谢物。因此，我们缺乏有效的机制来刺激这些休眠基因的合成，这些休眠基因是合成这些额外的、潜在的新抗生素所必需的。在共培养中生长的细菌似乎上调了它们次级代谢物的产生，以充当物种间的信号线索。我们的中心假设是，共培养将刺激产生不是在单一培养中产生的分子，其中一些可能是以前没有特征的抗生素。我们将使用以下方法来检验这一假设。在目标1中，我们将使用成像质谱学来广泛地检测在共培养中产生的特定化合物的产生，而在目标2中，我们将采取有针对性的方法，使用生物信息学来鉴定编码蛋白质的细菌菌株，并使用共培养来刺激它们的产生。最后，在目标3中，我们将测试在前两个目标中获得的各种共培养诱导的代谢物对人类病原体的抗生素活性。最有希望的线索将被分离和化学鉴定。我们的研究建议利用微生物共培养来诱导细菌代谢物的产生，以鉴定新发现的抗生素。最终，这项研究的结果将有助于我们的长期目标，即确保微生物继续为我们提供必要的构建块，以补充我们用于治疗的抗生素武器库。

 DESCRIPTION (provided by applicant) There has been a frightening rise in the incidence of disease-causing bacteria resistant to commonly used antibiotics. We therefore urgently need to identify additional molecules to use as antibiotics. Bacteria themselves have historically been the best source for antibiotics and other related 'secondary metabolites'. While the most common and abundant microbial antibiotics have already been harvested as "low-hanging fruit," microbes remain a deep potential source of new secondary metabolites. A critical barrier to obtaining these compounds, however, has been that bacteria rarely produce their full repertoire of secondary metabolites when cultured in the laboratory. What we lack therefore are efficient mechanisms to stimulate the synthesis of these dormant genes required to synthesize these additional, potentially novel, antibiotics. Bacteria grown in co-culture appear to up-regulate their production of secondary metabolites to act as interspecies signaling cues. Our central hypothesis is that co-culture will stimulate the production of molecules not produced in mono-culture, some of which may be previously uncharacterized antibiotics. We will test this hypothesis using the following approaches. In Aim 1 we will use imaging mass spectrometry to broadly detect the production of compounds produced specifically in co-culture, while in Aim 2 we will take a targeted approach and use bioinformatics to identify bacterial strains encoding proteins predicted to create novel secondary metabolites, and use co-culture to stimulate their production. Finally, in Aim 3 we will test the various co-culture-induced metabolites obtained in the previous two aims for antibiotic activity against human pathogens. The most promising leads will be isolated and chemically identified. Our research proposes to exploit microbial co-culture to elicit the production of bacterial metabolites to identify newly discovered antibiotics. Ultimately, the results from this research will contribute to our long-term goal of ensuring that microbes continue to provide us with the building blocks necessary to replenish our arsenal of antibiotics for therapeutic use.