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

2020 ◽  
Author(s):  
Su Hyun Park ◽  
Hyung-Sae Kim ◽  
Prakash Jyoti Kalita ◽  
Sang-Bong Choi
Keyword(s):  
Protein Structure ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Chara Corallina ◽  
Random Coil ◽  
Rrna Processing ◽  
High Coverage ◽  
Morphological Defects ◽  
Pumilio Proteins

Abstract 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.

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

2020 ◽  
Author(s):  
Su Hyun Park ◽  
Hyung-Sae Kim ◽  
Prakash Jyoti Kalita ◽  
Sang-Bong Choi
Keyword(s):  
Protein Structure ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Chara Corallina ◽  
Random Coil ◽  
Rrna Processing ◽  
High Coverage ◽  
Morphological Defects ◽  
Pumilio Proteins

Abstract 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.

scholarly journals Structural and functional similarities and differences in nucleolar Pumilio RNA-binding proteins between Arabidopsis and Charophyte Chara corallina

2019 ◽  
Author(s):  
Su Hyun Park ◽  
Hyung-Sae im ◽  
Prakash Jyoti Kalita ◽  
Sang-Bong Choi
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Tertiary Structure ◽  
Rna Binding Proteins ◽  
Chara Corallina ◽  
Its2 Sequence ◽  
Random Coil ◽  
Rrna Processing ◽  
Morphological Defects ◽  
Pumilio Proteins

Abstract Background: Pumilio RNA-binding proteins are evolutionarily conserved throughout all eukaryotes and are involved in RNA decay, transport, and translation repression in the cytoplasm. Even though a majority of Pumilio proteins function in the cytoplasm, two nucleolar forms have been reported to have a function in rRNA processing in Arabidopsis. Chara is known to be most closely related to land plants as it shares several characteristics with modern embryophytes. Results: In this study, we identified two putative nucleolar Pumilio protein genes, ChPUM2 and ChPUM3 , from the transcriptome of Chara corallina . Of the two ChPUM proteins, ChPUM2 was the most similar to Arabidopsis APUM23 in the amino acid sequence (27% identity and 45% homology) and the predicted protein structure, 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 APUM23-GFP and 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'-GAAUUGACGG) for APUM23 was conserved in Arabidopsis and Chara, whereas a target region of ITS2 pre-rRNA for APUM24 was 156 nt longer in Chara than in Arabidopsis. 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 as ChPUM3 has a long random coil in this domain. Conclusions: Our results indicate that ChPUM2 has evolutionarily maintained functions in Arabidopsis, while ChPUM3 is not functional in Arabidopsis, most likely due to the long target ITS2 sequence of Arabidopsis and the distinct tertiary structure from Arabidopsis homologue APUM24.

scholarly journals A deep learning framework to predict binding preference of RNA constituents on protein surface

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jordy Homing Lam ◽  
Yu Li ◽  
Lizhe Zhu ◽  
Ramzan Umarov ◽  
Hanlun Jiang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Protein Structure ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Preference ◽  
Rna Backbone ◽  
Binding Pockets ◽  
Rna Interaction

Abstract Protein-RNA interaction plays important roles in post-transcriptional regulation. However, the task of predicting these interactions given a protein structure is difficult. Here we show that, by leveraging a deep learning model NucleicNet, attributes such as binding preference of RNA backbone constituents and different bases can be predicted from local physicochemical characteristics of protein structure surface. On a diverse set of challenging RNA-binding proteins, including Fem-3-binding-factor 2, Argonaute 2 and Ribonuclease III, NucleicNet can accurately recover interaction modes discovered by structural biology experiments. Furthermore, we show that, without seeing any in vitro or in vivo assay data, NucleicNet can still achieve consistency with experiments, including RNAcompete, Immunoprecipitation Assay, and siRNA Knockdown Benchmark. NucleicNet can thus serve to provide quantitative fitness of RNA sequences for given binding pockets or to predict potential binding pockets and binding RNAs for previously unknown RNA binding proteins.

scholarly journals A Novel Small-Subunit Processome Assembly Intermediate That Contains the U3 snoRNP, Nucleolin, RRP5, and DBP4

2009 ◽  
Vol 29 (11) ◽  
pp. 3007-3017 ◽  
Author(s):  
Amy Jane Turner ◽  
Andrew Alexander Knox ◽  
José-Luis Prieto ◽  
Brian McStay ◽  
Nicholas James Watkins
Keyword(s):  
Ribosome Biogenesis ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Dynamic Structure ◽  
Small Subunit ◽  
Rrna Processing ◽  
Key Factors ◽  
Assembly Intermediate ◽  
Ssu Processome

ABSTRACT Eukaryotic 18S rRNA processing is mediated by the small subunit (SSU) processome, a machine comprised of the U3 small nucleolar RNP (U3 snoRNP), tUTP, bUTP, MPP10, and BMS1/RCL1 subcomplexes. We report that the human SSU processome is a dynamic structure with the recruitment and release of subcomplexes occurring during the early stages of ribosome biogenesis. A novel 50S U3 snoRNP accumulated when either pre-rRNA transcription was blocked or the tUTP proteins were depleted. This complex did not contain the tUTP, bUTP, MPP10, and BMS1/RCL1 subcomplexes but was associated with the RNA-binding proteins nucleolin and RRP5 and the RNA helicase DBP4. Our data suggest that the 50S U3 snoRNP is an SSU assembly intermediate that is likely recruited to the pre-rRNA through the RNA-binding proteins nucleolin and RRP5. We predict that nucleolin is only transiently associated with the SSU processome and likely leaves the complex not long after 50S U3 snoRNP recruitment. The nucleolin-binding site potentially overlaps that of several other key factors, and we propose that this protein must leave the SSU processome for pre-rRNA processing to occur.

Sign in / Sign up

Export Citation Format

Share Document