Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.
Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.
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DOI：
10.1186/1471-2180-9-185
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发表时间：
2009-09-01
期刊：
影响因子：
4.2
通讯作者：
Hackett M
中科院分区：
文献类型：
--
作者：
Hendrickson EL;Xia Q;Wang T;Lamont RJ;Hackett M
牙龈卟啉单胞菌是一种与牙周病相关的革兰氏阴性细胞内病原体。我们之前报道过全细胞定量蛋白质组学分析，以研究当生物体从细胞外生活方式转变为细胞内生活方式时毒力因子的差异表达。入侵菌株牙龈假单胞菌ATCC 33277的原始结果是使用当时可用的基因组序列菌株W83 [GenBank: AE015924]获得的。我们利用最近发表的菌株ATCC 33277的基因组注释重新处理了数据集[GenBank: AP009380]，并基于代谢途径而不是单个蛋白质分析了差异丰度。使用菌株ATCC 33277注释对1266个蛋白进行定性检测，这些蛋白在人牙龈上皮细胞和暴露于牙龈细胞培养基的对照组中内化18小时，比W83注释提高了7%。内化细胞显示，从天冬酰胺/天冬氨酸氨基酸到ATP的能量通路中蛋白质的丰度增加。产生一种短链脂肪酸丙酸的途径丰度增加，而产生另一种短链脂肪酸丁酸的途径丰度减少。翻译机制，包括核糖体蛋白和tRNA合成酶，显示出蛋白质相对丰度的显著增加，负责转录的蛋白质也是如此。ATCC 33277特异性基因组注释的使用提高了蛋白质组覆盖范围，包括在蛋白质鉴定方面定性观察到的蛋白质数量和在计算丰度比方面定量观察到的蛋白质数量。途径分析显示，在没有显著生长的情况下，总体蛋白质合成和转录机制显著增加。这些结果表明，与细胞外环境相比，宿主细胞内部提供了一个更丰富的能量环境。细胞内牙龈卟啉卟啉菌产生细胞毒性脂肪酸的变化可能在毒力中起作用。此外，尽管菌株W83和33277之间存在广泛的基因组重排，但在肽水平上存在足够的序列相似性，因此当使用异源菌株注释基因组作为数据库检索参考时，蛋白质组学丰度趋势在很大程度上是准确的。
Porphyromonas gingivalis is a Gram-negative intracellular pathogen associated with periodontal disease. We have previously reported on whole-cell quantitative proteomic analyses to investigate the differential expression of virulence factors as the organism transitions from an extracellular to intracellular lifestyle. The original results with the invasive strain P. gingivalis ATCC 33277 were obtained using the genome sequence available at the time, strain W83 [GenBank: AE015924]. We present here a re-processed dataset using the recently published genome annotation specific for strain ATCC 33277 [GenBank: AP009380] and an analysis of differential abundance based on metabolic pathways rather than individual proteins. Qualitative detection was observed for 1266 proteins using the strain ATCC 33277 annotation for 18 hour internalized P. gingivalis within human gingival epithelial cells and controls exposed to gingival cell culture medium, an improvement of 7% over the W83 annotation. Internalized cells showed increased abundance of proteins in the energy pathway from asparagine/aspartate amino acids to ATP. The pathway producing one short chain fatty acid, propionate, showed increased abundance, while that of another, butyrate, trended towards decreased abundance. The translational machinery, including ribosomal proteins and tRNA synthetases, showed a significant increase in protein relative abundance, as did proteins responsible for transcription. Use of the ATCC 33277 specific genome annotation resulted in improved proteome coverage with respect to the number of proteins observed both qualitatively in terms of protein identifications and quantitatively in terms of the number of calculated abundance ratios. Pathway analysis showed a significant increase in overall protein synthetic and transcriptional machinery in the absence of significant growth. These results suggest that the interior of host cells provides a more energy rich environment compared to the extracellular milieu. Shifts in the production of cytotoxic fatty acids by intracellular P. gingivalis may play a role in virulence. Moreover, despite extensive genomic re-arrangements between strains W83 and 33277, there is sufficient sequence similarity at the peptide level for proteomic abundance trends to be largely accurate when using the heterologous strain annotated genome as the reference for database searching.
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影响因子：
7.6
作者：
Hendrickson EL;Lamont RJ;Hackett M
通讯作者：
Hackett M
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3.2
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