Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
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DOI：
10.1101/gr.1589103
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发表时间：
2003-10-01
期刊：
影响因子：
7
通讯作者：
Koonin, EV
中科院分区：
文献类型：
--
作者：
Krylov, DM;Wolf, YI;Koonin, EV
谱系特异性基因丢失在很大程度上解释了基因组之间基因库的差异，特别是在真核生物中。我们从7个完整的真核生物基因组中推导出了真核生物直链组（KOG）基因丢失的简约方案。这种情况涉及真菌、线虫和昆虫的大量基因丢失。基于这种进化的情况下，主要的真核生物门之间的分歧时间的估计，我们引入了一个数字的措施，基因丢失的倾向（PGL）。我们探讨了基因在进化中丢失的倾向（PGL值），蛋白质序列差异，基因敲除对适应性的影响，蛋白质-蛋白质相互作用的数量以及KOG中基因的表达水平之间的联系。PGL和这些变量中的每一个之间的显着相关性进行了检测。在真核生物进化中丢失倾向较低的基因在其蛋白质序列中积累较少的取代，并且往往是生物体生存力所必需的，往往是高度表达的，并且具有许多相互作用伴侣。PGL与基因可免除性和交互性的相关性比序列进化率的相关性更强。因此，基因在进化过程中丢失的倾向似乎是其生物学重要性的直接反映。
Lineage-specific gene loss, to a large extent, accounts for the differences in gene repertoires between genomes, particularly among eukaryotes. We derived a parsimonious scenario of gene losses for eukaryotic orthologous groups (KOGs) from seven complete eukaryotic genomes. The scenario involves substantial gene loss in fungi, nematodes, and insects. Based on this evolutionary scenario and estimates of the divergence times between major eukaryotic phyla, we introduce a numerical measure, the propensity for gene loss (PGL). We explore the connection among the propensity of a gene to be lost in evolution (PGL value), protein sequence divergence, the effect of gene knockout on fitness, the number of protein-protein interactions, and expression level for the genes in KOGs. Significant correlations between PGL and each of these variables were detected. Genes that have a lower propensity to be lost in eukaryotic evolution accumulate fewer substitutions in their protein sequences and tend to be essential for the organism viability, tend to be highly expressed, and have many interaction partners. The dependence between PGL and gene dispensability and interactivity is much stronger than that for sequence evolution rate. Thus, propensity of a gene to be lost during evolution seems to be a direct reflection of its biological importance.