Duan Bingbing, Qiu Chenxi, Lockless Steve W, Sze Sing-Hoi, Kaplan Craig D
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
Department of Genetics, Harvard Medical School, Boston, MA 02215, USA.
Genetics. 2024 Oct 24;228(4). doi: 10.1093/genetics/iyae172.
RNA polymerase II (Pol II) has a highly conserved domain, the trigger loop (TL), that controls transcription fidelity and speed. We previously probed pairwise genetic interactions between residues within and surrounding the TL for the purpose of understand functional interactions between residues and to understand how individual mutants might alter TL function. We identified widespread incompatibility between TLs of different species when placed in the Saccharomyces cerevisiae Pol II context, indicating species-specific interactions between otherwise highly conserved TLs and its surroundings. These interactions represent epistasis between TL residues and the rest of Pol II. We sought to understand why certain TL sequences are incompatible with S. cerevisiae Pol II and to dissect the nature of genetic interactions within multiply substituted TLs as a window on higher order epistasis in this system. We identified both positive and negative higher-order residue interactions within example TL haplotypes. Intricate higher-order epistasis formed by TL residues was sometimes only apparent from analysis of intermediate genotypes, emphasizing complexity of epistatic interactions. Furthermore, we distinguished TL substitutions with distinct classes of epistatic patterns, suggesting specific TL residues that potentially influence TL evolution. Our examples of complex residue interactions suggest possible pathways for epistasis to facilitate Pol II evolution.
RNA聚合酶II（Pol II）有一个高度保守的结构域，即触发环（TL），它控制转录保真度和速度。我们之前探究了TL内部及周围残基之间的成对遗传相互作用，目的是了解残基之间的功能相互作用，以及单个突变体如何改变TL功能。当置于酿酒酵母Pol II环境中时，我们发现不同物种的TL之间存在广泛的不相容性，这表明在其他方面高度保守的TL与其周围环境之间存在物种特异性相互作用。这些相互作用代表了TL残基与Pol II其余部分之间的上位性。我们试图了解为什么某些TL序列与酿酒酵母Pol II不相容，并剖析多重取代TL内遗传相互作用的本质，以此作为该系统中高阶上位性的一个窗口。我们在示例TL单倍型中确定了正向和负向的高阶残基相互作用。有时，只有通过对中间基因型的分析才能明显看出由TL残基形成的复杂高阶上位性，这突出了上位性相互作用的复杂性。此外，我们区分了具有不同上位性模式类别的TL替代，这表明了可能影响TL进化的特定TL残基。我们复杂残基相互作用的例子表明了上位性促进Pol II进化的可能途径。
