Immunoregulation, Institute of Biomedical Technology, FI-33014 University of Tampere, Finland.
BMC Genomics. 2011 Dec 20;12:618. doi: 10.1186/1471-2164-12-618.
Subtilisin/kexin-like proprotein convertase (PCSK) enzymes have important regulatory function in a wide variety of biological processes. PCSKs proteolytically process at a target sequence that contains basic amino acids arginine and lysine, which results in functional maturation of the target protein. In vitro assays have showed significant biochemical redundancy between the seven family members, but the phenotypes of PCSK deficient mice and patients carrying an inactive PCSK allele argue for a specific biological function. Modeling the structures of individual PCSK enzymes has offered little insights into the specificity determinants. However, previous studies have shown that there can be a coordinated expression between a PCSK and its target molecule. Here, we have surveyed the putative PCSK target proteins using genome-wide expression correlation analysis and cleavage site prediction algorithms.
We first performed a gene expression correlation analysis over the whole genome for all PCSK enzymes. PCSKs were found to cluster differently based on the strength of correlations. The screen for putative PCSK target proteins showed a significant enrichment (p-values from 1.2e-4 to < 1.0e-10) of putative targets among the most positively correlating genes for most PCSKs. Interestingly, there was no enrichment in putative targets among the genes that correlated positively with the biologically redundant PCSK7, whereas PCSK5 showed an inverse correlation. PCSKs also showed a highly variable degree of shared target genes that were identified by expression correlation and cleavage site prediction. Multiple alignments were used to evaluate the putative targets to pinpoint the important residues for the substrate recognition. Finally, we validated our approach and identified biochemically PAPPA1 and ADAMTS6 as novel targets for FURIN proteolytic activity.
Most PCSK enzymes display strong positive expression correlation with predicted target proteins in our genome-wide analysis. We also show that expression correlation screen combined with a cleavage site-prediction analysis can be used to identify novel bona fide target molecules for PCSKs. Exploring the positively correlating genes can thus offer additional insights into the biology of proprotein convertases.
枯草溶菌素/激肽释放酶原(proprotein convertase, PCSK)酶在广泛的生物学过程中具有重要的调节功能。PCSKs 对含有精氨酸和赖氨酸等碱性氨基酸的靶序列进行蛋白水解处理，从而使靶蛋白发挥功能成熟。体外试验表明，这 7 种家族成员之间存在显著的生化冗余性，但 PCSK 缺陷小鼠的表型和携带无活性 PCSK 等位基因的患者表明其具有特定的生物学功能。对单个 PCSK 酶的结构建模几乎无法提供对特异性决定因素的深入了解。然而，先前的研究表明，PCSK 和其靶分子之间可能存在协调表达。在这里，我们使用全基因组表达相关性分析和切割位点预测算法来研究潜在的 PCSK 靶蛋白。
我们首先对所有 PCSK 酶进行了全基因组基因表达相关性分析。根据相关性的强弱，PCSK 聚类方式不同。针对潜在 PCSK 靶蛋白的筛选显示，对于大多数 PCSK，在与最正相关基因中，潜在靶蛋白显著富集（p 值从 1.2e-4 到<1.0e-10）。有趣的是，在与生物冗余性 PCSK7 呈正相关的基因中没有潜在靶蛋白的富集，而 PCSK5 则呈负相关。PCSK 还显示出高度可变的共享靶基因程度，这些基因通过表达相关性和切割位点预测来识别。多重比对用于评估潜在靶标，以确定用于底物识别的重要残基。最后，我们验证了我们的方法，并鉴定了 PAPPA1 和 ADAMTS6 作为 FURIN 蛋白水解活性的新靶标。
在我们的全基因组分析中，大多数 PCSK 酶与预测的靶蛋白表现出强烈的正表达相关性。我们还表明，表达相关性筛选与切割位点预测分析相结合可用于鉴定 PCSK 的新的真正靶分子。探索正相关基因可以为蛋白水解酶的生物学提供更多的见解。
