Arabidopsis EMB2788/Npa1L1 is critical for pre-rRNA processing, ribosome biogenesis, and embryo development

Ribosome assembly, a fundamental process for cellular functions, requires the precise processing of precursor rRNA (pre-rRNA) into mature rRNAs, a transformation guided by ribosome biogenesis factors (RBFs). While this process is well characterized in yeast and mammals, the roles of RBFs in pre-rRNA processing in plants remain poorly understood. Here, we report the characterization of Arabidopsis EMB2788, previously linked to embryonic development but functionally uncharacterized. We identified EMB2788 as the homolog of yeast nucleolar pre-ribosomal-associated protein 1 (Npa1p), a key pre-rRNA processing regulator, and named it Npa1L1. npa1l1 embryos exhibited severe defects from the late globular stage onward, including altered cell division planes, slowed division rates, and a consequent disruption of bilateral symmetry, accompanied by delayed endosperm development, although a small proportion of embryos developed into morphologically abnormal seedlings. Npa1L1 was likely a nucleolar protein and its loss of function led to an increased abundance of 40S subunits and a reduced abundance of 60S subunits and 80S monosomes. Molecular analysis showed pronounced accumulation of 35S pre-rRNA and 18S rRNA precursors (P-A₃) and a reduction in mature 18S rRNA levels. Furthermore, co-immunoprecipitation experiments indicated that Npa1L1 physically interacted with ribosome biogenesis factors, including the DEAD-box RNA helicases RH7 and RH27, and the GTPase NSN1. Collectively, our findings uncover that Npa1L1 is a crucial ribosome biogenesis factor in Arabidopsis that contributes to pre-rRNA processing, ribosomal subunit homeostasis, and embryo development. Nevertheless, the precise function of Npa1L1 in rRNA processing, and whether it differs from that of yeast Npa1p, requires further investigation.