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Background  Pumilio RNA-binding proteins are evolutionarily conserved throughout eukaryotes and are involved in RNA decay, transport, and translation repression in the cytoplasm. Although a majority of Pumilio proteins function in the cytoplasm, two nucleolar forms have been reported to have a function in rRNA processing in Arabidopsis. The species of the genus  Chara  have been known to be most closely related to land plants, as they share several characteristics with modern Embryophyta.    Results  In this study, we identified two putative nucleolar Pumilio protein genes, namely,  ChPUM2  and  ChPUM3 , from the transcriptome of  Chara corallina . Of the two ChPUM proteins, ChPUM2 was most similar in amino acid sequence (27% identity and 45% homology) and predicted protein structure to Arabidopsis APUM23, while ChPUM3 was similar to APUM24 (35% identity and 54% homology). The transient expression of  35S:ChPUM2-RFP  and  35S:ChPUM3-RFP  showed nucleolar localization of fusion proteins in tobacco leaf cells, similar to the expression of  35S:APUM23-GFP  and  35S:APUM24-GFP . Moreover,  35S:ChPUM2  complemented the morphological defects of the  apum23  phenotypes but not those of  apum24,  while  35S:ChPUM3  could not complement the  apum23  and  apum24  mutants. Similarly, the  35S:ChPUM2/apum23  plants rescued the pre-rRNA processing defect of  apum23 , but  35S:ChPUM3/apum24   +/−   plants did not rescue that of  apum24 . Consistent with these complementation results, a known target RNA-binding sequence at the end of the 18S rRNA (5′-GGAAUUGACGG) for APUM23 was conserved in Arabidopsis and  C. corallina , whereas a target region of ITS2 pre-rRNA for APUM24 was 156 nt longer in  C. corallina  than in  A. thaliana . Moreover, ChPUM2 and APUM23 were predicted to have nearly identical structures, but ChPUM3 and APUM24 have different structures in the 5th C-terminal Puf RNA-binding domain, which had a longer random coil in ChPUM3 than in APUM24.    Conclusions  ChPUM2 of  C. corallina  was functional in Arabidopsis, similar to APUM23, but ChPUM3 did not substitute for APUM24 in Arabidopsis. Protein homology modeling showed high coverage between APUM23 and ChPUM2, but displayed structural differences between APUM24 and ChPUM3. Together with the protein structure of ChPUM3 itself, a short ITS2 of Arabidopsis pre-rRNA may interrupt the binding of ChPUM3 to 3′-extended 5.8S pre-rRNA.

bmc plant biology

Structural and functional similarities and differences in nucleolar Pumilio RNA-binding proteins between Arabidopsis and the charophyte Chara corallina