Defining Evolutionary Trajectories: Molecular adaptation to antibiotic resistance

定义进化轨迹：抗生素耐药性的分子适应

基本信息

批准号：
10610338
负责人：
Yousif Shamoo
金额：
$ 35.36万
依托单位：
RICE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-07-15 至 2025-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10610338
关键词：
Affinity Antibiotic Resistance Antibiotic Therapy Antibiotics Binding Biochemical Biochemical Pathway Biochemistry Biophysics Bioreactors Categories Cell Death Induction Cell Wall Cells Centers for Disease Control and Prevention (U.S.)Critical Illness Critical Pathways Daptomycin Development Drug usage Emulsions Enterococcus Enterococcus faecalis Enterococcus faecium Environment Enzyme Kinetics Event Evolution Frequencies Genetic Genome Genomics Goals Homeostasis Hospitals Immunocompromised Host Infection Knock-out Life Ligand Binding Ligands Light Link Maps Membrane Methods Microfluidics Modern Medicine Molecular Molecular Analysis Morphology Multi-Drug Resistance Multiple Bacterial Drug Resistance Mutation Nature Nosocomial Infections Oils Operative Surgical Procedures Organism Pathway interactions Patients Pharmaceutical Preparations Phenotype Physicians Population Proliferating Proteins Public Health Regulatory Pathway Resistance Resistance development Resources Signal Pathway Signal Transduction Streptomyces Stress System Techniques Vancomycin Vancomycin resistant enterococcus Variant Water Work X-Ray Crystallography antimicrobial biophysical analysis biophysical properties clinically relevant combat drug discovery effectiveness evaluation enzyme activity improved innovation multi-drug resistant pathogen new technology novel novel strategies pathogen pathogenic bacteria protein structure function reproductive success resistance mechanism resistant strain success transcriptome sequencing

项目摘要

Antibiotic resistance among bacterial pathogens remains one of the great challenges confronting public health in the world today. The widespread use of antibiotics has facilitated the rise of multi-drug resistant pathogens that threaten to undermine the remarkable success of modern medicine. The Centers for Disease Control and Prevention have identified multi-drug resistant enterococci as a “Serious Threat” requiring prompt and sustained activity to limit proliferation. Daptomycin is a frontline antibiotic with efficacy against Gram positive organisms and is used with increasing frequency against multi-drug resistant enterococci such as vancomycin-resistant enterococci (VREs). The goal of this proposal is to comprehensively map the evolutionary trajectories leading to DAP resistance in Enterococcus faecium and elucidate how the identified changes in protein structure-function establish the physicochemical basis for the observed resistance phenotypes. We use quantitative experimental evolution in a novel, continuous culture bioreactor system to identify and rank the most important evolutionary trajectories leading to resistance. Based upon these results, we then characterize the most relevant proteins and pathways to daptomycin resistance using a combination of biochemical and structural approaches that link the change in biophysical properties to resistance. Techniques include X-ray crystallography, enzyme activity, ligand affinity, protein stability studies, RNAseq, qPCR, and others. This approach seeks to determine, not only the biochemical basis for resistance, but also those candidate proteins and pathways that would be well suited for the development of a new class of co-drugs that would target and delay the development of resistance. Our studies can also provide valuable molecular indicators of emerging resistance. Using our expertise in experimental evolution, we have also developed a new approach to harness both the power of evolution and the largely unexplored biochemical diversity and killing strategies of one of Nature's best antibiotic producing organisms: Streptomyces. We use experimental evolution within micro-emulsion droplets to produce selection conditions to identify variants of S. roseosporus (the “Predator”) that have improved their ability to kill a VRE strain (the “Prey”). Within each micro-droplet, we trap the two populations (Predator and a Prey). If the Predator can adapt to kill the Prey, the adapted Predator has a significant resource advantage, and increased reproductive success, over the un-adapted Predator. Taken together, this project takes a multi-pronged approach to uncovering the mechanisms and physicochemical basis for the evolution of antibiotic resistance and extends experimental evolution to include a novel method for discovering new antimicrobials.

细菌病原体的抗生素耐药性仍然是公众面临的巨大挑战之一当今世界的健康状况，抗生素的广泛使用促进了多重耐药性的增加。威胁破坏现代医学取得的巨大成功的病原体。疾病控制和预防已将多重耐药肠球菌确定为“严重威胁” 达托霉素是一种一线抗生素，需要迅速和持续的活性来限制增殖。对革兰氏阳性菌具有功效，并且针对多种药物的使用频率越来越高耐药肠球菌，例如耐万古霉素肠球菌 (VRE) 该提案的目标是全面绘制屎肠球菌 DAP 耐药性的进化轨迹并阐明已识别的蛋白质结构-功能变化如何建立理化我们在新颖的实验中使用定量实验进化作为观察到的抗性表型的基础。连续培养生物反应器系统，用于识别和排序最重要的进化轨迹然后根据这些结果，我们描述了最相关的蛋白质和耐药性。使用生化和结构方法相结合的达托霉素抗性途径将生物物理特性的变化与耐药性联系起来，包括 X 射线晶体学、酶活性、配体亲和力、蛋白质稳定性研究、RNAseq、qPCR 等。不仅试图确定耐药性的生化基础，而且还确定那些候选蛋白质以及非常适合开发一类新型联合药物的途径我们的研究还可以提供有价值的分子。利用我们在实验进化方面的专业知识，我们还发现了新出现的耐药性的指标。开发了一种新方法来利用进化的力量和很大程度上未经探索的自然界最好的抗生素生产生物体之一的生化多样性和杀灭策略：我们利用微乳液液滴内的实验进化来产生选择。鉴定玫瑰孢链球菌（“捕食者”）变种的条件，这些变种提高了其杀伤能力在每个微滴中，我们捕获了两个种群（捕食者和猎物）。如果捕食者能够适应杀死猎物，则适应后的捕食者具有显着的资源优势，与未适应的捕食者相比，增加了繁殖成功率。多管齐下的方法来揭示进化的机制和物理化学基础抗生素耐药性并扩展实验进化以包括发现抗生素耐药性的新方法新的抗菌剂。

项目成果

期刊论文数量（34）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Small changes in enzyme function can lead to surprisingly large fitness effects during adaptive evolution of antibiotic resistance.

在抗生素耐药性的适应性进化过程中，酶功能的微小变化可能会导致惊人的巨大适应性效应。

DOI：
10.1073/pnas.1209335110
发表时间：
2012
期刊：
Proceedings of the National Academy of Sciences of the United States of America
影响因子：
11.1
作者：
Walkiewicz,Katarzyna;BenitezCardenas,AndresS;Sun,Christine;Bacorn,Colin;Saxer,Gerda;Shamoo,Yousif
通讯作者：
Shamoo,Yousif

Asymmetric Alkylation of Anthrones, Enantioselective Total Synthesis of (-)- and (+)-Viridicatumtoxins B and Analogues Thereof: Absolute Configuration and Potent Antibacterial Agents.

DOI：
10.1021/jacs.6b12654
发表时间：
2017-03-15
期刊：
Journal of the American Chemical Society
影响因子：
15
作者：
Nicolaou KC;Liu G;Beabout K;McCurry MD;Shamoo Y
通讯作者：
Shamoo Y

Daptomycin-resistant Enterococcus faecalis diverts the antibiotic molecule from the division septum and remodels cell membrane phospholipids.

达托霉素耐药粪肠球菌将抗生素分子从分裂隔膜转移并重塑细胞膜磷脂。

DOI：
10.1128/mbio.00281-13
发表时间：
2013
期刊：
mBio
影响因子：
6.4
作者：
Tran,TrucT;Panesso,Diana;Mishra,NagendraN;Mileykovskaya,Eugenia;Guan,Ziqianq;Munita,JoseM;Reyes,Jinnethe;Diaz,Lorena;Weinstock,GeorgeM;Murray,BarbaraE;Shamoo,Yousif;Dowhan,William;Bayer,ArnoldS;Arias,CesarA
通讯作者：
Arias,CesarA

Indirect Enrichment of Desirable, but Less Fit Phenotypes, from a Synthetic Microbial Community Using Microdroplet Confinement.

使用微滴限制从合成微生物群落中间接富集所需但不太适合的表型。

DOI：
10.1021/acssynbio.3c00008
发表时间：
2023
期刊：
ACS synthetic biology
影响因子：
4.7
作者：
GanigaPrabhakar,Ramya;Fan,Gaoyang;Alnahhas,RazanN;Hirning,AndrewJ;Bennett,MatthewR;Shamoo,Yousif
通讯作者：
Shamoo,Yousif

Targeting cell membrane adaptation as a novel antimicrobial strategy.