Phenotype accessibility and noise in random threshold gene regulatory networks.
Phenotype accessibility and noise in random threshold gene regulatory networks.
复制标题
DOI：
10.1371/journal.pone.0119972
复制
发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Feldman MW
中科院分区：
文献类型：
--
作者：
Pinho R;Garcia V;Feldman MW
进化需要生物群体中的表型变异，以便选择发挥作用。生物体发育中的基因调控过程影响生物体的表型多样性。由于只有一小部分的所有可能的表型被预测到开发结束时访问，生物体可能会进化策略，使用环境的线索和噪音一样的波动，以产生额外的表型多样性，从而提高适应的速度。我们使用了生物体发育的通用模型-基因调控网络-来研究基因表达状态（即表型）的不同水平的噪音如何影响获得新的，独特的表型，从而影响表型多样性。我们研究了生物体可能采取的其他策略，以获得更大的表型多样性：通过增加基因组或基因表达状态的数量。这是针对不同类型的基因调控网络进行的，这些网络允许对基因表达产生不同水平的调控影响，或者更有可能产生稳定的表型。我们发现，如果基因表达是二元的，增加噪音水平通常会降低所有网络类型的表型可访问性。如果考虑更多的基因表达状态，如果允许三个或四个基因表达状态，并且如果群体中有足够的不同调控网络，则噪声可以适度提高发现的速度。这些结果与所分析的网络类型无关，并且对不同的噪声实现具有鲁棒性。因此，为了增加基因调控网络中可访问表型的数量，需要满足非常特定的条件。如果生物体发育中涉及的不同调控网络的数量足够大，并且获得更多基因或对其表达状态进行微调对生物体来说是昂贵的，那么噪音可以用于允许获得更独特的表型。
Evolution requires phenotypic variation in a population of organisms for selection to function. Gene regulatory processes involved in organismal development affect the phenotypic diversity of organisms. Since only a fraction of all possible phenotypes are predicted to be accessed by the end of development, organisms may evolve strategies to use environmental cues and noise-like fluctuations to produce additional phenotypic diversity, and hence to enhance the speed of adaptation. We used a generic model of organismal development --gene regulatory networks-- to investigate how different levels of noise on gene expression states (i.e. phenotypes) may affect access to new, unique phenotypes, thereby affecting phenotypic diversity. We studied additional strategies that organisms might adopt to attain larger phenotypic diversity: either by augmenting their genome or the number of gene expression states. This was done for different types of gene regulatory networks that allow for distinct levels of regulatory influence on gene expression or are more likely to give rise to stable phenotypes. We found that if gene expression is binary, increasing noise levels generally decreases phenotype accessibility for all network types studied. If more gene expression states are considered, noise can moderately enhance the speed of discovery if three or four gene expression states are allowed, and if there are enough distinct regulatory networks in the population. These results were independent of the network types analyzed, and were robust to different implementations of noise. Hence, for noise to increase the number of accessible phenotypes in gene regulatory networks, very specific conditions need to be satisfied. If the number of distinct regulatory networks involved in organismal development is large enough, and the acquisition of more genes or fine tuning of their expression states proves costly to the organism, noise can be useful in allowing access to more unique phenotypes.
登录
查看更多内容
影响因子：
64.8
作者：
Alon, U;Surette, MG;Leibler, S
通讯作者：
Leibler, S
DOI：
10.1098/rspb.1979.0086
发表时间：
1979-01-01
期刊：
PROCEEDINGS OF THE ROYAL SOCIETY SERIES B-BIOLOGICAL SCIENCES
影响因子：
--
作者：
GOULD, SJ;LEWONTIN, RC
通讯作者：
LEWONTIN, RC
影响因子：
64.8
作者：
Barkai, N;Leibler, S
通讯作者：
Leibler, S
DOI：
10.1073/pnas.231499798
发表时间：
2001-11-20
影响因子：
11.1
作者：
Edelman, GM;Gally, JA
通讯作者：
Gally, JA
影响因子：
56.9
作者：
Lee, TI;Rinaldi, NJ;Young, RA
通讯作者：
Young, RA