State Key Laboratory of Rice Biology and Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China; Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan.
Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan.
Comput Biol Chem. 2020 Jun;86:107245. doi: 10.1016/j.compbiolchem.2020.107245. Epub 2020 Mar 4.
Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from rice plant as the reference. Re-sequencing results revealed that the genome of strain AU6208 comprised 96 contigs corresponding to a 6.1 Mbp genome of the strain AU6208, with 5322 coding sequences and 68.2 % GC content; this is much larger compared to the genome previously sequenced by us and described by Seo et al (2015), which was reported to be 4.1 Mbp comprising >1200 contigs, 4361 coding sequences, and 67.31 % GC content. Moreover, this updated genome shares >80 % identity to the 7.2 Mbp genome of BGR1, which encodes 6491 coding sequences and has 68.3 % GC content. Further computational analysis revealed that the strain AU6208 encodes several bacteriocin biosynthesis genes, antibiotic, as well as virulent genes such as toxoflavin genes, which included 425 specialty genes and 12 toxoflavin genes. Upon further characterization, 12 toxoflavins (ToxA, B, C, D, E, F, G, H, I, J, TofI, and TofR) were found in AU6208 with 70-100 % sequence, family, and domain similarity with that of BGR1. Upon comparison with BGR1, the structural characterizations of selected toxoflavin genes (ToxB, ToxC, ToxG, H, and TofI) revealed variations in 2D and 3D structures such as differences in α-helix, β-sheets, loops, physiological properties of proteins, RMSD values, etc. These variations may play significant role in different mode of action in different hosts thereby indicating that in addition to their respective hosts, toxoflavins could also contribute to exploit other hosts across the kingdom. In addition to understanding the epidemiology of strain AU6208, this updated genomics data will also unfold the pathogenicity of bacteria in diversity of various hosts and anti-virulence.
引起水稻细菌性穗枯病的主要病原体 Burkholderia glumae 已被报道为慢性感染患者中的机会性病原体。本研究旨在重新测序临床分离株 B. glumae 菌株 AU6208，并使用来自水稻植株的 B. glumae 菌株 BGR1 作为参考比较分析其基因组。重测序结果表明，菌株 AU6208 的基因组由 96 个连续序列组成，对应于菌株 AU6208 的 6.1 Mbp 基因组，包含 5322 个编码序列和 68.2% 的 GC 含量；与我们之前测序并由 Seo 等人描述的基因组（2015 年）相比，这要大得多，该基因组报告为 4.1 Mbp，包含>1200 个连续序列、4361 个编码序列和 67.31% 的 GC 含量。此外，这个更新的基因组与 BGR1 的 7.2 Mbp 基因组共享>80%的同一性，BGR1 编码 6491 个编码序列，GC 含量为 68.3%。进一步的计算分析表明，菌株 AU6208 编码几种细菌素生物合成基因、抗生素以及毒黄素基因等毒力基因，包括 425 个特殊基因和 12 个毒黄素基因。进一步的表征发现，在 AU6208 中发现了 12 种毒黄素（ToxA、B、C、D、E、F、G、H、I、J、TofI 和 TofR），与 BGR1 的序列、家族和结构域相似性为 70-100%。与 BGR1 相比，选择的毒黄素基因（ToxB、ToxC、ToxG、H 和 TofI）的结构特征揭示了 2D 和 3D 结构的差异，如 α-螺旋、β-折叠、环、蛋白质的生理特性、RMSD 值等。这些差异可能在不同宿主中的不同作用模式中发挥重要作用，从而表明除了各自的宿主外，毒黄素还可能有助于利用其他宿主。除了了解菌株 AU6208 的流行病学外，这个更新的基因组学数据还将揭示细菌在各种宿主中的多样性和抗毒力的致病性。
