Duplicate gene enrichment and expression pattern diversification in multicellularity.
Duplicate gene enrichment and expression pattern diversification in multicellularity.
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DOI：
10.1093/nar/gks464
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发表时间：
2012-09
影响因子：
14.9
通讯作者：
Wang D
中科院分区：
文献类型：
--
作者：
Padawer T;Leighty RE;Wang D
多细胞生物与单细胞生物中重复基因的富集，以及由此产生的旁系同源物（由重复基因编码的蛋白质），增强了基因组功能创新。本研究定量分析了多细胞性与基因富集、表达模式多样性之间的关系，旨在更好地理解多细胞性的基因组基础。将特定细胞中的Partial丰度与单细胞蛋白质组和多细胞生物的整个蛋白质组中的Partial丰度进行比较。芽殖酵母，酿酒酵母和线虫，秀丽隐杆线虫，在特定的细胞中表达的基因集是可用的，分别被用作单细胞和多细胞模型。在两个物种的整个蛋白质组和特定的C中，粒子数（K）分布[P（k）]遵循幂律关系[P（k）<$k−α]。线虫细胞常数α的值可以用来衡量paraerodynamic丰度;值越高，paraerodynamic丰度越低。在整个蛋白质组中，C. elegans（1.74）比S. cerevisiae（2.34），定量多细胞物种中旁系同源物的富集。我们还发现，幂律关系适用于特定的C。线虫细胞值得注意的是，特定细胞中的α值更高，与S.啤酒。因此，在特定细胞中的parabolic丰度较低，与单细胞物种相当。此外，一个基因的表达水平在不同的C. elegans细胞与其寄生虫计数正相关，这进一步被不同组织中的人类基因表达模式所证实。总之，这些结果定量和机械地建立丰富的旁系同源物与多样化的表达模式作为多细胞性的基因组和进化基础。
The enrichment of duplicate genes, and therefore paralogs (proteins coded by duplicate genes), in multicellular versus unicellular organisms enhances genomic functional innovation. This study quantitatively examined relationships among paralog enrichment, expression pattern diversification and multicellularity, aiming to better understand genomic basis of multicellularity. Paralog abundance in specific cells was compared with those in unicellular proteomes and the whole proteomes of multicellular organisms. The budding yeast, Saccharomyces cerevisiae and the nematode, Caenorhabditis elegans, for which the gene sets expressed in specific cells are available, were used as uni and multicellular models, respectively. Paralog count (K) distributions [P(k)] follow a power-law relationship [P(k) ∝ k−α] in the whole proteomes of both species and in specific C. elegans cells. The value of the constant α can be used as a gauge of paralog abundance; the higher the value, the lower the paralog abundance. The α-value is indeed lower in the whole proteome of C. elegans (1.74) than in S. cerevisiae (2.34), quantifying the enrichment of paralogs in multicellular species. We also found that the power-law relationship applies to the proteomes of specific C. elegans cells. Strikingly, values of α in specific cells are higher and comparable to that in S. cerevisiae. Thus, paralog abundance in specific cells is lower and comparable to that in unicellular species. Furthermore, how much the expression level of a gene fluctuates across different C. elegans cells correlates positively with its paralog count, which is further confirmed by human gene-expression patterns across different tissues. Taken together, these results quantitatively and mechanistically establish enrichment of paralogs with diversifying expression patterns as genomic and evolutionary basis of multicellularity.
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DOI：
10.1093/bioinformatics/btn214
发表时间：
2008-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capra JA;Singh M
通讯作者：
Singh M
影响因子：
8
作者：
Kalinina, OV;Mironov, AA;Rakhmaninova, AB
通讯作者：
Rakhmaninova, AB
影响因子：
56.9
作者：
Lynch, M;Conery, JS
通讯作者：
Conery, JS
影响因子：
14.9
作者：
Pruitt KD;Tatusova T;Klimke W;Maglott DR
通讯作者：
Maglott DR
影响因子：
56.9
作者：
Barabási, AL;Albert, R
通讯作者：
Albert, R