Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea.
Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
Nucleic Acids Res. 2023 Aug 11;51(14):7424-7437. doi: 10.1093/nar/gkad489.
Gene families divergently evolve and become adapted as different genes with specific structures and functions in living organisms. We performed comprehensive structural and functional analyses of Zinc-finger homeodomain genes (ZF-HDs), including Mini zinc-finger genes (MIFs) and Zinc-finger with homeodomain genes (ZHDs), displaying competitive functions each other. Intensive annotation updates for 90 plant genomes verified that most MIFs (MIF-Is) exhibited distinct motif compositions from ZHDs, although some MIFs (MIF-Zs) contained ZHD-specific motifs. Phylogenetic analyses suggested that MIF-Zs and ZHDs originated from the same ancestral gene, whereas MIF-Is emerged from a distinct progenitor. We used a gene-editing system to identify a novel function of MIF-Is in rice: regulating the surface material patterns in anthers and pollen through transcriptional regulation by interacting ZHDs. Kingdom-wide investigations determined that (i) ancestral MIFs diverged into MIF-Is and MIF-Zs in the last universal common ancestor, (ii) integration of HD into the C-terminal of MIF-Zs created ZHDs after emergence of green plants and (iii) MIF-Is and ZHDs subsequently expanded independently into specific plant lineages, with additional formation of MIF-Zs from ZHDs. Our comprehensive analysis provides genomic evidence for multiphase evolution driving divergent selection of ZF-HDs.
基因家族在进化过程中会发生分歧，并成为具有特定结构和功能的不同基因，适应生物体的生存需求。我们对锌指同源结构域基因（ZF-HD）进行了全面的结构和功能分析，包括迷你锌指基因（MIFs）和锌指同源结构域基因（ZHDs），它们彼此之间存在竞争作用。对 90 个植物基因组进行的强化注释更新证实，尽管一些 MIFs（MIF-Zs）包含 ZHD 特异性基序，但大多数 MIFs（MIF-Is）表现出明显不同的基序组成。系统发育分析表明，MIF-Zs 和 ZHDs 起源于同一祖先基因，而 MIF-Is 则起源于一个不同的祖先。我们使用基因编辑系统鉴定了 MIF-Is 在水稻中的一个新功能：通过与 ZHD 相互作用，转录调控花药和花粉的表面物质模式。对整个生物界的调查确定了：（i）在最后普遍共同祖先中，祖先 MIFs 分化为 MIF-Is 和 MIF-Zs；（ii）HD 整合到 MIF-Zs 的 C 末端后，在绿色植物出现后形成了 ZHDs；（iii）MIF-Is 和 ZHDs 随后在特定的植物谱系中独立扩张，而 MIF-Zs 则是从 ZHDs 中进一步形成的。我们的综合分析提供了基因组证据，证明了 ZF-HD 的多阶段进化驱动了分歧选择。
