Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia, Medellín, Colombia.
Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México.
Appl Microbiol Biotechnol. 2021 Dec;105(23):8805-8822. doi: 10.1007/s00253-021-11659-3. Epub 2021 Oct 30.
Actinobacteria embroil Gram-positive microbes with high guanine and cytosine contents in their DNA. They are the source of most antimicrobials of bacterial origin utilized in medicine today. Their genomes are among the richest in novel secondary metabolites with high biotechnological potential. Actinobacteria reveal complex patterns of evolution, responses, and adaptations to their environment, which are not yet well understood. We analyzed three novel plant isolates and explored their habitat adaptation, evolutionary patterns, and potential secondary metabolite production. The phylogenomically characterized isolates belonged to Actinoplanes sp. TFC3, Streptomyces sp. L06, and Embleya sp. NF3. Positively selected genes, relevant in strain evolution, encoded enzymes for stress resistance in all strains, including porphyrin, chlorophyll, and ubiquinone biosynthesis in Embleya sp. NF3. Streptomyces sp. L06 encoded for pantothenate and proteins for CoA biosynthesis with evidence of positive selection; furthermore, Actinoplanes sp. TFC3 encoded for a c-di-GMP synthetase, with adaptive mutations. Notably, the genomes harbored many genes involved in the biosynthesis of at least ten novel secondary metabolites, with many avenues for future new bioactive compound characterization-specifically, Streptomyces sp. L06 could make new ribosomally synthesized and post-translationally modified peptides, while Embleya sp. NF3 could produce new non-ribosomal peptide synthetases and ribosomally synthesized and post-translationally modified peptides. At the same time, TFC3 has particularly enriched in terpene and polyketide synthases. All the strains harbored conserved genes in response to diverse environmental stresses, plant growth promotion factors, and degradation of various carbohydrates, which supported their endophytic lifestyle and showed their capacity to colonize other niches. This study aims to provide a comprehensive estimation of the genomic features of novel Actinobacteria. It sets the groundwork for future research into experimental tests with new bioactive metabolites with potential application in medicine, biofertilizers, and plant biomass residue utilization, with potential application in medicine, as biofertilizers and in plant biomass residues utilization. KEY POINTS: • Potential of novel environmental bacteria for secondary metabolites production • Exploring the genomes of three novel endophytes isolated from a medicinal tree • Pan-genome analysis of Actinobacteria genera.
放线菌使 DNA 中含有高比例鸟嘌呤和胞嘧啶的革兰氏阳性微生物相互纠缠。它们是当今医学中使用的大多数细菌来源抗菌药物的来源。它们的基因组是具有高生物技术潜力的新型次生代谢产物中最丰富的。放线菌表现出复杂的进化模式、对环境的反应和适应，这些目前还不太了解。我们分析了三个新的植物分离物，探讨了它们的栖息地适应、进化模式和潜在的次生代谢产物生产。经过系统发育特征分析的分离物属于游动放线菌属 sp. TFC3、链霉菌属 sp. L06 和 Embleya 属 sp. NF3。正选择基因在所有菌株中编码与压力相关的酶，这些酶参与菌株的进化，包括 Embleya 属 sp. NF3 中的卟啉、叶绿素和泛醌生物合成。链霉菌属 sp. L06 编码泛酸和 CoA 生物合成的蛋白质，具有正选择的证据；此外，游动放线菌属 sp. TFC3 编码 c-di-GMP 合成酶，具有适应性突变。值得注意的是，这些基因组中含有许多参与至少十种新型次生代谢产物生物合成的基因，为未来新生物活性化合物的表征提供了许多途径-特别是，链霉菌属 sp. L06 可以产生新的核糖体合成和翻译后修饰的肽，而 Embleya 属 sp. NF3 可以产生新的非核糖体肽合成酶和核糖体合成和翻译后修饰的肽。同时，TFC3 特别富含萜烯和聚酮合酶。所有菌株都含有对各种环境压力、植物生长促进因子和各种碳水化合物降解的保守基因，这支持了它们的内生生活方式，并显示了它们在其他生态位中定殖的能力。本研究旨在对新型放线菌的基因组特征进行全面评估。它为未来的实验研究奠定了基础，这些研究涉及具有潜在医学应用、生物肥料和植物生物质残渣利用价值的新型生物活性代谢产物。
