Exploitation of Burkholderia bacteria as novel antibiotic producers using a genome mining approach

使用基因组挖掘方法将伯克霍尔德氏菌开发为新型抗生素生产者

• 批准号: BB/L021692/1
• 负责人: Eshwar Mahenthiralingam
• 金额: $ 43.09万
• 依托单位: CARDIFF UNIVERSITY
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL021692%2F1
• 关键词: Exploitation; Burkholderia; bacteria; novel; antibiotic

USING NOVEL DISCOVERY TOOLS AND PRODUCER BACTERIA TO IDENTIFY RESISTANCE-BUSTING ANTIBIOTICSThere is an urgent need to discover and develop new antibiotics to treat resistant infections caused by superbugs. Most of the antibiotics we use today are produced by one group of soil bacteria, the Streptomyces. Researchers at Cardiff University discovered that another group of bacteria, known as Burkholderia, produce novel antibiotics that kill superbugs that have become resistant to current antibiotics such as Methicillin Resistant Staphylococcus aureus (MRSA). To enable clinical and commercial development, the chemical structures of antibiotics must be determined to see if they are novel compounds. Via collaboration with experts at the University of Warwick's Department of Chemistry, we have determined complete structures for one Burkholderia antibiotic, enacyloxin IIa, and partially determined the structures of two novel antibiotics, gladiolin and vietnamycin. Purifying and determining the chemical structures of antibiotics takes time and considerable expertise, therefore researchers are now using a new tool for antibiotic discovery called genome mining. This approach takes the entire genetic code (genome sequence) of an antibiotic producing bacterium and then searches it for genes involved in the production of novel antibiotics. The Wellcome Trust Sanger Institute (WTSI) are pioneers in bacterial genome sequencing and have new technology called Pacific Biosciences sequencing, which is ideally suited to rapid bacterial genome determination in a single sequence run. In collaboration with researchers at WTSI, we sequenced the genome of the gladiolin producing strain and were able to identify the genes involved in production of this antibiotic. Using this extra sequence information, we can now determine the full structure of gladiolin which is needed to take the antibiotic forward into clinical development. Overall, our preliminary research has shown that Burkholderia are an untapped, promising source of new antibiotics to combat multidrug-resistant superbugs. To determine if Burkholderia can be as successful as the Streptomyces bacteria which produce the majority of the antibiotics we use today, we will use genome mining as a new Burkholderia antibiotic discovery tool, and aim to: 1. Genome sequence 24 antibiotic producing Burkholderia using the Pacific Biosciences sequencing technology. Firstly, to advance characterization of vietnamycin, our anti-MRSA antibiotic, the Burkholderia strain producing this antibiotic will be sequenced. 23 more strains which kill current drug resistant bacteria will then be selected from our large collection. In total, the 24 antibiotic producing Burkholderia genomes will create a unique library of DNA for genome mining and discovery of new antibiotics.2. Fully identify the structure for gladiolin and vietnamycin, using a combination of chemistry and genetic analysis of their genomes and production pathways.3. Carry out a unique genome mining survey of Burkholderia antibiotic capacity using the genomes of the 24 strains known to have novel resistance-busting activity. The first two goals of the grant described above will create the genome mining data and also train the researchers on the grant in all the skills necessary to implement this new approach to antibiotic discovery. We will also investigate if "silent pathways" which encode novel antibiotics within the genomes of these Burkholderia can be switched on.4. The last objective of our research will be to prepare a panel of five novel antibiotics to take forward into preclinical development as drugs to combat resistance. In addition to gladiolin and vietnamycin, we will use the information from genome mining to complete the structure and activity analysis of three further novel Burkholderia antibiotics.

使用新的发现工具和生产者芽孢杆菌来鉴定耐药性破坏抗生素迫切需要发现和开发新的抗生素来治疗由超级细菌引起的耐药性感染。我们今天使用的大多数抗生素都是由一组土壤细菌产生的，链霉菌。卡迪夫大学的研究人员发现，另一组细菌，称为伯克霍尔德氏菌，产生新型抗生素，杀死超级细菌，这些超级细菌已经对目前的抗生素产生耐药性，如耐甲氧西林金黄色葡萄球菌（MRSA）。为了能够进行临床和商业开发，必须确定抗生素的化学结构，以确定它们是否是新化合物。通过与沃里克大学化学系的专家合作，我们已经确定了一种伯克霍尔德氏菌抗生素enacloxin IIa的完整结构，并部分确定了两种新型抗生素唐菖蒲素和越南霉素的结构。纯化和确定抗生素的化学结构需要时间和大量的专业知识，因此研究人员现在正在使用一种新的抗生素发现工具，称为基因组挖掘。这种方法需要抗生素生产细菌的整个遗传密码（基因组序列），然后搜索它的基因参与生产新的抗生素。Wellcome Trust桑格研究所（WTSI）是细菌基因组测序领域的先驱，拥有名为Pacific Biosciences测序的新技术，非常适合在单次测序中快速确定细菌基因组。与WTSI的研究人员合作，我们对唐菖蒲素生产菌株的基因组进行了测序，并能够鉴定出参与这种抗生素生产的基因。利用这些额外的序列信息，我们现在可以确定唐菖蒲素的完整结构，这是将抗生素推向临床开发所必需的。总体而言，我们的初步研究表明，伯克霍尔德氏菌是一种尚未开发的，有希望的新抗生素来源，可用于对抗多重耐药超级细菌。为了确定伯克霍尔德氏菌是否能像产生我们今天使用的大多数抗生素的链霉菌一样成功，我们将使用基因组挖掘作为一种新的伯克霍尔德氏菌抗生素发现工具，并旨在：1。使用Pacific Biosciences测序技术对产生24种抗生素的伯克霍尔德氏菌进行基因组测序。首先，为了进一步表征我们的抗MRSA抗生素越那霉素，将对产生该抗生素的伯克霍尔德氏菌菌株进行测序。然后将从我们的大量收集中选择另外23种杀死当前耐药细菌的菌株。总的来说，24个产生抗生素的伯克霍尔德氏菌基因组将创建一个独特的DNA文库，用于基因组挖掘和发现新的抗生素。利用化学和遗传学相结合的方法对唐菖蒲素和越南霉素的基因组和生产途径进行分析，全面鉴定其结构.使用已知具有新型耐药性破坏活性的24种菌株的基因组，对伯克霍尔德氏菌抗生素能力进行独特的基因组挖掘调查。上述赠款的前两个目标将创建基因组挖掘数据，并培训研究人员掌握实施这种抗生素发现新方法所需的所有技能。我们还将研究这些伯克霍尔德氏菌基因组中编码新型抗生素的“沉默途径”是否可以被打开。我们研究的最后一个目标是准备一个由五种新型抗生素组成的小组，作为对抗耐药性的药物进入临床前开发。除了唐菖蒲素和越南霉素，我们将使用基因组挖掘的信息来完成三种新型伯克霍尔德氏菌抗生素的结构和活性分析。

项目成果

Diene incorporation by a dehydratase domain variant in modular polyketide synthases.

• DOI: 10.1038/s41589-022-01127-y
• 发表时间: 2022-12
• 期刊: Nature chemical biology
• 影响因子: 14.8
• 作者: Hobson C;Jenner M;Jian X;Griffiths D;Roberts DM;Rey-Carrizo M;Challis GL
• 通讯作者: Challis GL

Discovery and Biosynthesis of Bolagladins: Unusual Lipodepsipeptides from Burkholderia gladioli Clinical Isolates*.

• DOI: 10.1002/anie.202009110
• 发表时间: 2020-11-23
• 期刊: Angewandte Chemie (International ed. in English)
• 作者: Dashti Y;Nakou IT;Mullins AJ;Webster G;Jian X;Mahenthiralingam E;Challis GL
• 通讯作者: Challis GL

Understanding biosynthetic protein-protein interactions.

了解生物合成蛋白质-蛋白质相互作用。

• DOI: 10.1039/c8np90037j
• 发表时间: 2018
• 期刊: Natural product reports
• 影响因子: 11.9
• 作者: Ackerley DF