ABSTRACT
BACKGROUND: Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. RESULTS: We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. CONCLUSIONS: Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.
Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/genetics , Gene Expression Regulation, Plant , Poly(A)-Binding Proteins/metabolism , Protein Biosynthesis , RNA, Messenger/chemistry , RNA, Messenger/metabolism , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/physiology , Base Composition , Genes, Plant , Guanosine/analysis , Poly(A)-Binding Protein II/genetics , Poly(A)-Binding Protein II/metabolism , Poly(A)-Binding Protein II/physiology , Poly(A)-Binding Proteins/genetics , Poly(A)-Binding Proteins/physiology , Protein BindingABSTRACT
Poly(A)-binding proteins (PABPs) are important to eukaryotic gene expression. In the nucleus, the PABP PABPN1 is thought to function in polyadenylation of pre-mRNAs. Deletion of fission yeast pab2, the homolog of mammalian PABPN1, results in transcripts with markedly longer poly(A) tails, but the nature of the hyperadenylated transcripts and the mechanism that leads to RNA hyperadenylation remain unclear. Here we report that Pab2 functions in the synthesis of noncoding RNAs, contrary to the notion that PABPs function exclusively on protein-coding mRNAs. Accordingly, the absence of Pab2 leads to the accumulation of polyadenylated small nucleolar RNAs (snoRNAs). Our findings suggest that Pab2 promotes poly(A) tail trimming from pre-snoRNAs by recruiting the nuclear exosome. This work unveils a function for the nuclear PABP in snoRNA synthesis and provides insights into exosome recruitment to polyadenylated RNAs.
Subject(s)
Exosomes/physiology , Poly(A)-Binding Protein II/physiology , RNA, Small Nucleolar/biosynthesis , Schizosaccharomyces pombe Proteins/physiology , Schizosaccharomyces/metabolism , Cell Nucleus/genetics , Cell Nucleus/metabolism , Genome, Fungal , Oligonucleotide Array Sequence Analysis , Poly(A)-Binding Protein II/genetics , Polyadenylation , Schizosaccharomyces/genetics , Schizosaccharomyces pombe Proteins/geneticsSubject(s)
Host-Pathogen Interactions , Molecular Chaperones/physiology , Orthomyxoviridae/genetics , Orthomyxoviridae/physiology , Virus Replication , Cleavage And Polyadenylation Specificity Factor/physiology , Genome, Viral/genetics , Nuclear Proteins/physiology , Poly(A)-Binding Protein II/physiology , RNA-Binding Proteins , Signal Transduction/physiology , Transcription Factors/physiology , Transcription, Genetic/genetics , Viral Nonstructural Proteins , Virus Replication/genetics , alpha Karyopherins/physiologyABSTRACT
Poly (A) tails are found at the 3' ends of almost all eukaryotic mRNAs. They are bound by two different poly (A) binding proteins, PABPC in the cytoplasm and PABPN1 in the nucleus. PABPC functions in the initiation of translation and in the regulation of mRNA decay. In both functions, an interaction with the m7G cap at the 5' end of the message plays an important role. PABPN1 is involved in the synthesis of poly (A) tails, increasing the processivity of poly (A) polymerase and contributing to defining the length of a newly synthesized poly (A) tail.
