PDF(Pubmed)
Abstract：
BACKGROUND: Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paenibacillus genomes encompass a considerable array of antibiotic biosynthetic gene clusters (BGCs), rendering these species as good candidates for genome-driven novel antibiotic exploration. Nevertheless, BGCs within Paenibacillus genomes have not been extensively studied.
RESULTS: We conducted an analysis of 554 Paenibacillus genome sequences, sourced from the National Center for Biotechnology Information database, with a focused investigation involving 89 of these genomes via antiSMASH. Our analysis unearthed a total of 848 BGCs, of which 716 (84.4%) were classified as unknown. From the initial pool of 554 Paenibacillus strains, we selected 26 available in culture collections for an in-depth evaluation. Genomic scrutiny of these selected strains unveiled 255 BGCs, encoding non-ribosomal peptide synthetases, polyketide synthases, and bacteriocins, with 221 (86.7%) classified as unknown. Among these strains, 20 exhibited antimicrobial activity against the gram-positive bacterium Micrococcus luteus, yet only six strains displayed activity against the gram-negative bacterium Escherichia coli. We proceeded to focus on Paenibacillus brasilensis, which featured five new BGCs for further investigation. To facilitate detailed characterization, we constructed a mutant in which a single BGC encoding a novel antibiotic was activated while simultaneously inactivating multiple BGCs using a cytosine base editor (CBE). The novel antibiotic was found to be localized to the cell wall and demonstrated activity against both gram-positive bacteria and fungi. The chemical structure of the new antibiotic was elucidated on the basis of ESIMS, 1D and 2D NMR spectroscopic data. The novel compound, with a molecular weight of 926, was named bracidin.
CONCLUSIONS: This study outcome highlights the potential of Paenibacillus species as valuable sources for novel antibiotics. In addition, CBE-mediated dereplication of antibiotics proved to be a rapid and efficient method for characterizing novel antibiotics from Paenibacillus species, suggesting that it will greatly accelerate the genome-based development of new antibiotics.
RESULTS: We conducted an analysis of 554 Paenibacillus genome sequences, sourced from the National Center for Biotechnology Information database, with a focused investigation involving 89 of these genomes via antiSMASH. Our analysis unearthed a total of 848 BGCs, of which 716 (84.4%) were classified as unknown. From the initial pool of 554 Paenibacillus strains, we selected 26 available in culture collections for an in-depth evaluation. Genomic scrutiny of these selected strains unveiled 255 BGCs, encoding non-ribosomal peptide synthetases, polyketide synthases, and bacteriocins, with 221 (86.7%) classified as unknown. Among these strains, 20 exhibited antimicrobial activity against the gram-positive bacterium Micrococcus luteus, yet only six strains displayed activity against the gram-negative bacterium Escherichia coli. We proceeded to focus on Paenibacillus brasilensis, which featured five new BGCs for further investigation. To facilitate detailed characterization, we constructed a mutant in which a single BGC encoding a novel antibiotic was activated while simultaneously inactivating multiple BGCs using a cytosine base editor (CBE). The novel antibiotic was found to be localized to the cell wall and demonstrated activity against both gram-positive bacteria and fungi. The chemical structure of the new antibiotic was elucidated on the basis of ESIMS, 1D and 2D NMR spectroscopic data. The novel compound, with a molecular weight of 926, was named bracidin.
CONCLUSIONS: This study outcome highlights the potential of Paenibacillus species as valuable sources for novel antibiotics. In addition, CBE-mediated dereplication of antibiotics proved to be a rapid and efficient method for characterizing novel antibiotics from Paenibacillus species, suggesting that it will greatly accelerate the genome-based development of new antibiotics.
摘要：
背景：细菌抗菌素耐药性对人类构成严重威胁，迫切需要开发新的抗生素。基因组测序的最新进展为发现抗生素提供了新的途径。类芽孢杆菌基因组包含相当多的抗生素生物合成基因簇（BGC），使这些物种成为基因组驱动的新型抗生素探索的良好候选者。然而，尚未广泛研究类芽孢杆菌基因组中的BGC。
结果：我们对554个类芽孢杆菌基因组序列进行了分析，来自国家生物技术信息中心数据库，通过反SMASH对89个基因组进行了重点调查。我们的分析发现了总共848个BGC，其中716人（84.4%）被列为未知。从最初的554株类芽孢杆菌中，我们选择了26个文化收藏进行深入评估.对这些选定菌株的基因组审查揭示了255个BGC，编码非核糖体肽合成酶，聚酮化合物合酶，和细菌素,221（86.7%）被列为未知。在这些菌株中，20对革兰氏阳性菌黄体微球菌具有抗菌活性，然而，只有六株菌株显示出抗革兰氏阴性细菌大肠杆菌的活性。我们开始关注巴西芽孢杆菌，其中包括五个新的BGC进行进一步调查。为了便于详细表征，我们构建了一个突变体,其中编码一种新型抗生素的单一BGC被激活,同时使用胞嘧啶碱基编辑器(CBE)灭活多个BGC.发现新型抗生素位于细胞壁上，并具有针对革兰氏阳性细菌和真菌的活性。在ESIMS的基础上阐明了新抗生素的化学结构，1D和2DNMR光谱数据。新颖的化合物，分子量为926，被命名为bracidin。
结论：本研究结果突出了类芽孢杆菌作为新型抗生素有价值来源的潜力。此外,CBE介导的抗生素去复制被证明是一种快速有效的方法，用于表征类芽孢杆菌属的新型抗生素，这表明它将大大加速基于基因组的新抗生素的开发。
结果：我们对554个类芽孢杆菌基因组序列进行了分析，来自国家生物技术信息中心数据库，通过反SMASH对89个基因组进行了重点调查。我们的分析发现了总共848个BGC，其中716人（84.4%）被列为未知。从最初的554株类芽孢杆菌中，我们选择了26个文化收藏进行深入评估.对这些选定菌株的基因组审查揭示了255个BGC，编码非核糖体肽合成酶，聚酮化合物合酶，和细菌素,221（86.7%）被列为未知。在这些菌株中，20对革兰氏阳性菌黄体微球菌具有抗菌活性，然而，只有六株菌株显示出抗革兰氏阴性细菌大肠杆菌的活性。我们开始关注巴西芽孢杆菌，其中包括五个新的BGC进行进一步调查。为了便于详细表征，我们构建了一个突变体,其中编码一种新型抗生素的单一BGC被激活,同时使用胞嘧啶碱基编辑器(CBE)灭活多个BGC.发现新型抗生素位于细胞壁上，并具有针对革兰氏阳性细菌和真菌的活性。在ESIMS的基础上阐明了新抗生素的化学结构，1D和2DNMR光谱数据。新颖的化合物，分子量为926，被命名为bracidin。
结论：本研究结果突出了类芽孢杆菌作为新型抗生素有价值来源的潜力。此外,CBE介导的抗生素去复制被证明是一种快速有效的方法，用于表征类芽孢杆菌属的新型抗生素，这表明它将大大加速基于基因组的新抗生素的开发。
