植物基因表达调控与进化机制研究进展

doi:10.11983/CBB24175

摘要/Abstract

摘要： 功能基因表达是连接基因编码信息与蛋白质产物的一个基本生命过程, 基因表达水平被视为介于基因型与表现型之间的一种数量性状, 在植物应对气候和环境变化时发挥重要作用。该文首先系统综述了植物基因表达调控因子研究进展, 包括转录因子和小RNA等在基因表达调控中的作用。其次, 探讨了基于基因表达数据进行全基因组关联分析(GWAS)估计调控因子基因的表达数量性状基因座(eQTLs)位置以及该方法的局限性。随后从理论上分析了在突变、漂变、选择和迁移过程中的种内基因表达变异与检验方法, 在突变-漂变过程中以及在基于系统发育树的漂变-选择过程中的种间基因表达进化与检测方法。最后, 探讨了植物交配系统对基因表达进化的调控, 自交降低了有效群体大小、突变率、基因重组及外源花粉竞争, 改变了配子与合子阶段的自然选择功效等, 从而间接调控种内基因表达变异和种间基因表达进化。全文综合评述了目前的理论和实际研究进展及存在的问题, 有助于深入理解植物基因表达调控和进化机制。

关键词: 基因表达, 调控因子, 自然选择, 数量性状, 交配系统

Abstract: Functional gene expression is a basic life process that connects the coding information of a gene to protein products. The level of gene expression is considered as a quantitative trait between genotype and phenotype and plays an important role in response to climatic and environmental changes. First, we systematically summarize regulatory elements of gene expression in plant species and empirical evidence, including the effects of transcription factors and small RNAs on gene expression regulation. Second, this review discusses the eQTL mapping for regulatory elements of gene expression through gene expression-based genome-wide association study (GWAS) and the limitations of this method. This review analyzes the intraspecific variation in gene expression in theory under the processes of mutation, drift and selection and the testing methods. This review also analyzes the interspecific evolution of gene expression under the mutation and drift processes or under the phylogeny-based drift-selection processes and the testing methods. Finally, this review discusses the regulation of gene expression by the plant mating system. Selfing reduces the effective population size, mutation rate, recombination rate and competition from exogenous pollen, and changes the efficacy of natural selection in the gametophytic and sporophytic phases. Selfing regulates intraspecific gene expression variation and interspecific gene expression evolution. This review comprehensively comments on theoretical and practical research progress and existing questions, which aids in our deep understanding of plant gene expression regulation and evolution mechanisms.

Key words: gene expression, regulatory element, natural selection, quantitative trait, mating system

王子韵, 吕燕文, 肖钰, 吴超, 胡新生. 植物基因表达调控与进化机制研究进展. 植物学报, 2025, 60(4): 621-639.

Ziyun Wang, Yanwen Lü, Yu Xiao, Chao Wu, Xinsheng Hu. Advances in the Regulation and Evolutionary Mechanisms of Plant Gene Expression. Chinese Bulletin of Botany, 2025, 60(4): 621-639.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB24175

https://www.chinbullbotany.com/CN/Y2025/V60/I4/621

图/表 3

表1 基因表达相关调控因子与调控机制

Table 1 Regulatory factors and regulatory mechanisms of gene expression

调控过程	调控因子	调控机制
转录过程	转录因子、激活因子和阻碍物(蛋白质)	结合在靶基因启动子序列的结合位点, 将RNA聚合酶定位于启动子上, 控制基因的转录或转录效率, 或抑制转录启动
	内、外源激素	甾类和多肽激素与细胞质内或核内受体形成复合物, 调控某些基因转录
	IncRNA (>200 bp)	可与蛋白质(转录因子和组蛋白等)互作; 与DNA互作
	siRNA (20-25 bp)	干扰特定基因表达
转录后水平	miRNA (21-23 bp)	与靶mRNA互补配对, 抑制mRNA的翻译或降解靶mRNA
	lncRNA (>200 bp)	与RNA (mRNA、miRNA及其它lncRNA)互作
	酶蛋白	mRNA选择性和反剪接; RNA编辑
翻译过程	翻译起始因子等	翻译起始因子的可逆磷酸化; 非翻译区结构修饰变异
翻译后水平	肽链剪接酶、化学修饰酶等	新生肽链剪接, 化学修饰; 肽链折叠; 蛋白质更换等

图1 直系同源基因序列进化与直系同源基因表达进化比较 (A) 一对直系同源基因序列进化: 在中性过程下, 物种内基因序列上的突变数用Poisson分布描述, 每个子代物种累积突变数为 μ t , μ为每个碱基的突变率, t为两物种分化时间。在突变-漂变作用平衡时, 两直系同源基因的总突变数 K = 2 μ t; (B) 一对直系同源基因表达进化: 每个子代物种内, 1个基因表达受许多控制因子基因的影响, 在漂变过程中, 基因表达水平在物种内用Brownian运动分布表示, 在突变-漂变作用平衡时, 物种内基因表达的加性遗传方差为 2 N e σ m 2 , σ m 2为单世代突变产生的方差, 每个子代物种内积累的突变方差为 2 N e σ m 2 t , 两子代物种间基因表达水平均值的加性方差为 σ B 2 = 2 σ m 2 t 。

Figure 1 Comparison of the gene sequence evolution versus the gene expression evolution in a pair of orthologous genes (A) Gene sequence evolution of a pair of orthologous genes: under neutral processes, the number of mutations in a gene sequence within a species can be described by a Poisson distribution, the cumulative number of mutations in the gene sequence is approximated by μ t , where μis the mutation rate per base and t is the divergence time between two species. When mutation- drift equilibrium is reached, the total number of mutations in two orthologous genes is K = 2 μ t ; (B) Gene expression evolution of a pair of orthologous genes: gene expression in each descendant species is controlled by multiple orthologous genes for regulatory elements, under the process of genetic drift, the distribution of gene expression levels within a species can be described by the Brownian motion distribution, under equilibrium between mutation and drift effects, the additive genetic variance of gene expression within a species is equal to 2 N e σ m 2 , where σ m 2 is the variance generated by mutations per generation, the cumulative mutation variance within each descendant species is 2 N e σ m 2 t , and the additive genetic variance of the mean gene expression levels between two descendant species is σ B 2 = 2 σ m 2 t .

表2 基于种间基因表达进化的选择检验

Table 2 Selection tests based on the evolution of gene expression among species

检测方法	假设	参考文献
种内变异-种间分化比较 (纯突变过程)	H₀: 种间基因表达进化等于种内基因表达变异 H₁: 稳定选择或歧化选择	Oleksiak et al., 2002; Rifkin et al., 2003; Khaitovich et al., 2004; Lemos et al., 2005; Gilad et al., 2006
基于系统发育树 (考虑种间基因表达均值变异)	H₀: 种间基因表达进化遵循BM (Brownian-motion)过程, 类似于漂变过程; 只考虑基因表达均值特征 H₁: 种间基因表达进化遵循OU (Ornstein-Uhlenbeck)过程, 受稳定选择或定向选择	Butler and King, 2004; Bedford and Hartl, 2009; Gu, 2010
基于系统发育树 (考虑种内和种间基因表达变异)	H₀: 种内和种间基因表达进化遵循OU过程, 受稳定选择 H₁: 种内和种间基因表达进化遵循OU过程, 受定向选择	Rohlfs and Nielsen, 2015

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