Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species.
Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species.
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DOI：
10.1007/s00239-021-10022-4
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发表时间：
2021-10
影响因子：
3.9
通讯作者：
Rost B
中科院分区：
文献类型：
--
作者：
Marot-Lassauzaie V;Goldberg T;Armenteros JJA;Nielsen H;Rost B
蛋白质的天然亚细胞位置（也称为定位或细胞区室）是其作用最频繁的位置；它是蛋白质功能的一方面。十种真核模型生物的位置谱（即七个主要细胞区室中每个区室的蛋白质组比例）是否有所不同？由于位置的实验注释仍然存在偏差和不完整，我们需要预测方法来回答这个问题。经过系统偏差校正后，完整但有缺陷的预测方法似乎比不完整的更准确的实验数据更适合比较物种之间的位置光谱。这项工作比较了十种真核生物的位置光谱：智人（人类）、大猩猩（大猩猩）、黑猩猩（黑猩猩）、小家鼠（小鼠）、褐家鼠（大鼠）、黑腹果蝇（果蝇/醋蝇）、冈比亚按蚊（非洲疟蚊）、秀丽隐杆线虫（线虫）、酿酒酵母（面包酵母）和粟酒裂殖酵母（裂殖酵母）。最大的两类预计是细胞核和细胞质，合计占所有蛋白质的 47-62%，而 7-21% 的蛋白质预计位于质膜中，4-15% 被分泌。总体而言，预测的位置谱很大程度上相似。然而，详细而言，这些差异足以绘制树 (UPGMA) 和 2D (PCA) 地图，使用简单的欧几里得距离在七个州（位置类别）中关联十个生物体。基于简单预测位置谱的关系捕获了跨物种比较的各个方面，通常只有通过更详细的进化比较才能揭示。最有趣的是，已知的系统发育关系通过仅旁系同源树比通过仅直向同源树更好地再现。 在线版本包含可在 10.1007/s00239-021-10022-4 获取的补充材料。
The native subcellular location (also referred to as localization or cellular compartment) of a protein is the one in which it acts most frequently; it is one aspect of protein function. Do ten eukaryotic model organisms differ in their location spectrum, i.e., the fraction of its proteome in each of seven major cellular compartments? As experimental annotations of locations remain biased and incomplete, we need prediction methods to answer this question. After systematic bias corrections, the complete but faulty prediction methods appeared to be more appropriate to compare location spectra between species than the incomplete more accurate experimental data. This work compared the location spectra for ten eukaryotes: Homo sapiens (human), Gorilla gorilla (gorilla), Pan troglodytes (chimpanzee), Mus musculus (mouse), Rattus norvegicus (rat), Drosophila melanogaster (fruit/vinegar fly), Anopheles gambiae (African malaria mosquito), Caenorhabitis elegans (nematode), Saccharomyces cerevisiae (baker’s yeast), and Schizosaccharomyces pombe (fission yeast). The two largest classes were predicted to be the nucleus and the cytoplasm together accounting for 47–62% of all proteins, while 7–21% of the proteins were predicted in the plasma membrane and 4–15% to be secreted. Overall, the predicted location spectra were largely similar. However, in detail, the differences sufficed to plot trees (UPGMA) and 2D (PCA) maps relating the ten organisms using a simple Euclidean distance in seven states (location classes). The relations based on the simple predicted location spectra captured aspects of cross-species comparisons usually revealed only by much more detailed evolutionary comparisons. Most interestingly, known phylogenetic relations were reproduced better by paralog-only than by ortholog-only trees. The online version contains supplementary material available at 10.1007/s00239-021-10022-4.
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影响因子：
2.9
作者：
Bernhofer, Michael;Kloppmann, Edda;Reeb, Jonas;Rost, Burkhard
通讯作者：
Rost, Burkhard
影响因子：
3
作者：
Blum T;Briesemeister S;Kohlbacher O
通讯作者：
Kohlbacher O
影响因子：
14.9
作者：
Sonnhammer EL;Östlund G
通讯作者：
Östlund G
DOI：
10.1093/bioinformatics/btq706
发表时间：
2011-02-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Schliep KP
通讯作者：
Schliep KP
Wolf Psort：蛋白质定位预测因子。
影响因子：
14.9
作者：
Horton, Paul;Park, Keun-Joon;Obayashi, Takeshi;Fujita, Naoya;Harada, Hajime;Adams-Collier, C J;Nakai, Kenta
通讯作者：
Nakai, Kenta