Aceituno-Valenzuela Uri, Fontcuberta-Cervera Sara, Micol-Ponce Rosa, Sarmiento-Mañús Raquel, Ruiz-Bayón Alejandro, Ponce María Rosa
Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain.
Plant Physiol. 2024 Dec 24;197(1). doi: 10.1093/plphys/kiae641.
Zinc knuckle (ZCCHC) motif-containing proteins are present in unicellular and multicellular eukaryotes, and most ZCCHC proteins with known functions participate in the metabolism of various classes of RNA, such as mRNAs, ribosomal RNAs, and microRNAs. The Arabidopsis (Arabidopsis thaliana) genome encodes 69 ZCCHC-containing proteins; however, the functions of most remain unclear. One of these proteins, CAX-INTERACTING PROTEIN 4 (CXIP4, encoded by AT2G28910), has been classified as a PTHR31437 family member. This family includes human Splicing regulatory glutamine/lysine-rich protein 1 (SREK1)-interacting protein 1 (SREK1IP1), which is thought to function in pre-mRNA splicing and RNA methylation. Metazoan SREK1IP1-like and plant CXIP4-like proteins only share a ZCCHC motif, and their functions remain almost entirely unknown. Here, we studied two loss-of-function alleles of Arabidopsis CXIP4: cxip4-1 is likely null and shows early lethality, and cxip4-2 is hypomorphic and viable, with pleiotropic morphological defects. The cxip4-2 mutant exhibited deregulation of defense genes and upregulation of transcription factor genes, some of which might explain its developmental defects. The cxip4-2 mutant also exhibited increased intron retention events, being more evident in cxip4-1. The specific functions of misspliced genes, such as those involved in "gene silencing by DNA methylation" and "mRNA polyadenylation factor" suggest that CXIP4 has additional functions. In cxip4-2 plants, polyadenylated RNAs accumulate in the nucleus; these could be misspliced mRNAs. The CXIP4 protein localizes to the nucleus in a pattern resembling nuclear speckles rich in splicing factors. Therefore, CXIP4 is required for plant development and survival and mRNA maturation.
含锌指（ZCCHC）基序的蛋白质存在于单细胞和多细胞真核生物中，大多数具有已知功能的ZCCHC蛋白参与各类RNA的代谢，如信使核糖核酸（mRNA）、核糖体核糖核酸（rRNA）和微小核糖核酸（miRNA）。拟南芥（Arabidopsis thaliana）基因组编码69种含ZCCHC的蛋白质；然而，大多数蛋白质的功能仍不清楚。这些蛋白质之一，钙交换蛋白相互作用蛋白4（CXIP4，由AT2G28910编码），已被归类为PTHR31437家族成员。该家族包括人类富含谷氨酰胺/赖氨酸的剪接调节蛋白1（SREK1）相互作用蛋白1（SREK1IP1），被认为在信使核糖核酸前体（pre-mRNA）剪接和RNA甲基化中发挥作用。后生动物的SREK1IP1样蛋白和植物的CXIP4样蛋白仅共享一个ZCCHC基序，它们的功能几乎完全未知。在这里，我们研究了拟南芥CXIP4的两个功能缺失等位基因：cxip4-1可能是无效等位基因，表现出早期致死性，而cxip4-2是亚效等位基因且可存活，具有多效性形态缺陷。cxip4-2突变体表现出防御基因失调和转录因子基因上调，其中一些可能解释其发育缺陷。cxip4-2突变体还表现出内含子保留事件增加，在cxip4-1中更为明显。错配剪接基因的特定功能，如那些参与“DNA甲基化介导的基因沉默”和“mRNA聚腺苷酸化因子”的基因，表明CXIP4具有其他功能。在cxip4-2植物中，聚腺苷酸化的RNA在细胞核中积累；这些可能是错配剪接的mRNA。CXIP4蛋白以类似于富含剪接因子的核斑点的模式定位于细胞核。因此，CXIP4是植物发育、存活和mRNA成熟所必需的。
