Department of Biochemistry Ž Molecular Biology, Centre for High-throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia, V6T 1Z4 Canada.
BMC Genomics. 2011 Sep 16;12:450. doi: 10.1186/1471-2164-12-450.
As scientists continue to pursue various 'omics-based research, there is a need for high quality data for the most fundamental 'omics of all: genomics. The bacterium Paenibacillus larvae is the causative agent of the honey bee disease American foulbrood. If untreated, it can lead to the demise of an entire hive; the highly social nature of bees also leads to easy disease spread, between both individuals and colonies. Biologists have studied this organism since the early 1900s, and a century later, the molecular mechanism of infection remains elusive. Transcriptomics and proteomics, because of their ability to analyze multiple genes and proteins in a high-throughput manner, may be very helpful to its study. However, the power of these methodologies is severely limited without a complete genome; we undertake to address that deficiency here.
We used the Illumina GAIIx platform and conventional Sanger sequencing to generate a 182-fold sequence coverage of the P. larvae genome, and assembled the data using ABySS into a total of 388 contigs spanning 4.5 Mbp. Comparative genomics analysis against fully-sequenced soil bacteria P. JDR2 and P. vortex showed that regions of poor conservation may contain putative virulence factors. We used GLIMMER to predict 3568 gene models, and named them based on homology revealed by BLAST searches; proteases, hemolytic factors, toxins, and antibiotic resistance enzymes were identified in this way. Finally, mass spectrometry was used to provide experimental evidence that at least 35% of the genes are expressed at the protein level.
This update on the genome of P. larvae and annotation represents an immense advancement from what we had previously known about this species. We provide here a reliable resource that can be used to elucidate the mechanism of infection, and by extension, more effective methods to control and cure this widespread honey bee disease.
随着科学家们继续开展各种基于“组学”的研究，人们需要高质量的数据来支持最基本的“组学”：基因组学。幼虫芽孢杆菌是导致蜜蜂疾病美洲幼虫腐臭病的病原体。如果不进行治疗，它可能会导致整个蜂群死亡；蜜蜂高度的社会性也导致疾病在个体和群体之间很容易传播。自 20 世纪初以来，生物学家就一直在研究这种生物，一个世纪后，其感染的分子机制仍然难以捉摸。转录组学和蛋白质组学由于能够高通量地分析多个基因和蛋白质，因此可能对其研究非常有帮助。然而，如果没有完整的基因组，这些方法的威力将受到严重限制；我们在这里着手解决这一不足。
我们使用 Illumina GAIIx 平台和传统的 Sanger 测序技术，对幼虫芽孢杆菌基因组进行了 182 倍的序列覆盖，并使用 ABySS 将数据组装成总共 388 个跨越 450 万碱基对的 contigs。与完全测序的土壤细菌 P. JDR2 和 P. vortex 的比较基因组分析表明，保守性较差的区域可能包含潜在的毒力因子。我们使用 GLIMMER 预测了 3568 个基因模型，并根据 BLAST 搜索揭示的同源性对它们进行了命名；通过这种方式鉴定了蛋白酶、溶血因子、毒素和抗生素抗性酶。最后，质谱分析提供了实验证据，证明至少 35%的基因在蛋白质水平上表达。
幼虫芽孢杆菌基因组及其注释的这一更新代表了我们之前对该物种认识的巨大进步。我们提供了一个可靠的资源，可以用来阐明感染机制，并通过延伸，更有效地控制和治疗这种广泛存在的蜜蜂疾病。
