Differential effects of aromatic and charged residue substitutions in the RNA binding domains of the yeast Poly(A)-binding protein

The poly(A)-binding protein (PABP) is the major mRNA-binding protein in eukaryotes, and it is essential for viability of the yeast Saccharomyces cerevisiae. The amino acid sequence of the protein indicates that it consists of four ribonucleoprotein consensus sequence-containing RNA-binding domains (RBDs I, II, III, and IV) and a proline-rich auxiliary domain at the carboxyl terminus. We produced different parts of the S. cerevisiae PABP and studied their binding to poly(A) and other ribohomopolymers in vitro. We found that none of the individual RBDs of the protein bind poly(A) specifically or efficiently. Contiguous two-domain combinations were required for efficient RNA binding, and each pairwise combination (I/II, II/III, and III/IV) had a distinct RNA-binding activity. Specific poly(A)-binding activity was found only in the two amino-terminal RBDs (I/II) which, interestingly, are dispensable for viability of yeast cells, whereas the activity that is sufficient to rescue lethality of a PABP-deleted strain is in the carboxyl-terminal RBDs (III/IV). We conclude that the PABP is a multifunctional RNA-binding protein that has at least two distinct and separable activities: RBDs I/II, which most likely function in binding the PABP to mRNA through the poly(A) tail, and RBDs III/IV, which may function through binding either to a different part of the same mRNA molecule or to other RNA(s).

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The Xenopus laevis poly(A) binding protein is composed of multiple functionally independent RNA binding domains.

The EMBO Journal ◽

10.1002/j.1460-2075.1990.tb07582.x ◽

1990 ◽

Vol 9 (11) ◽

pp. 3699-3705 ◽

Cited By ~ 68

Author(s):

W. Nietfeld ◽

H. Mentzel ◽

T. Pieler

Keyword(s):

Xenopus Laevis ◽

Rna Binding ◽

Binding Protein ◽

Binding Domains ◽

Rna Binding Domains

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Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein

Protein Science ◽

10.1002/pro.543 ◽

2010 ◽

Vol 20 (1) ◽

pp. 118-130 ◽

Cited By ~ 43

Author(s):

Seisuke Yamashita ◽

Takashi Nagata ◽

Masahito Kawazoe ◽

Chie Takemoto ◽

Takanori Kigawa ◽

...

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Double Stranded Rna ◽

Binding Domains ◽

Tar Rna ◽

Rna Binding Domains

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C/EBPα acts as an RNA binding protein essential for its chromatin recruitment and promotes Macrophage differentiation

10.1101/2021.10.20.465166 ◽

2021 ◽

Author(s):

Yanzhou Zhang ◽

Mahmoud Bassal ◽

Daniel Friedrich ◽

Simone Ummarino ◽

Tom Verbiest ◽

...

Keyword(s):

Transcription Factor ◽

Dna Binding ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Specific Gene ◽

Macrophage Differentiation ◽

Binding Domains ◽

Rna Binding Domains ◽

Neutrophil Differentiation

C/EBPα has known to be a transcription factor that involved in Neutrophil differentiation for decades. However, exploring the Chromatin RNA Immunoprecipitation Sequencing (RIP), we discover that C/EBPα is a RNA binding protein mainly interacts with RNA introns. Structure study and RNA electrophoretic mobility shift assay (REMSA) show that C/EBPα interacts with RNA through two novel RNA binding domains distinct from its DNA binding domain. Mouse bone marrow transplantation and in vitro cytokine assay reveal that C/EBPα RNA binding is critical for Macrophage differentiation but not Neutrophil differentiation. Mechanically, RNA binding domains control specific gene transcription. In particular, PU.1 intron 4 RNA interacts with C/EBPα and recruit C/EBPα to its enhancer site, which facilitate PU.1 expression. Taken together, C/EBPα is demonstrated to be a RNA binding protein with unique function distinct from its DNA binding activity. Our finding transforms our knowledge of transcriptional regulation by transcription factor.

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The multiple RNA-binding domains of the mRNA poly(A)-binding protein have different RNA-binding activities

Molecular and Cellular Biology ◽

10.1128/mcb.11.7.3419-3424.1991 ◽

1991 ◽

Vol 11 (7) ◽

pp. 3419-3424

Author(s):

C G Burd ◽

E L Matunis ◽

G Dreyfuss

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Consensus Sequence ◽

Binding Activity ◽

Yeast Cells ◽

Yeast Saccharomyces Cerevisiae ◽

Amino Terminal ◽

Binding Domains ◽

Rna Binding Domains

The poly(A)-binding protein (PABP) is the major mRNA-binding protein in eukaryotes, and it is essential for viability of the yeast Saccharomyces cerevisiae. The amino acid sequence of the protein indicates that it consists of four ribonucleoprotein consensus sequence-containing RNA-binding domains (RBDs I, II, III, and IV) and a proline-rich auxiliary domain at the carboxyl terminus. We produced different parts of the S. cerevisiae PABP and studied their binding to poly(A) and other ribohomopolymers in vitro. We found that none of the individual RBDs of the protein bind poly(A) specifically or efficiently. Contiguous two-domain combinations were required for efficient RNA binding, and each pairwise combination (I/II, II/III, and III/IV) had a distinct RNA-binding activity. Specific poly(A)-binding activity was found only in the two amino-terminal RBDs (I/II) which, interestingly, are dispensable for viability of yeast cells, whereas the activity that is sufficient to rescue lethality of a PABP-deleted strain is in the carboxyl-terminal RBDs (III/IV). We conclude that the PABP is a multifunctional RNA-binding protein that has at least two distinct and separable activities: RBDs I/II, which most likely function in binding the PABP to mRNA through the poly(A) tail, and RBDs III/IV, which may function through binding either to a different part of the same mRNA molecule or to other RNA(s).

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